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BMRB: 15528

2JWN

Solution structure of the protease-resistent domain of Xenopus ePABP2

Authors

Song, J., Markley, J.L.

Assembly

ePABP2-trp

Entity

1. ePABP2-trp (polymer, Thiol state: all free), 124 monomers, 13533.10 × 2 Da Detail

AIAPCMQTTH SKMTAGAYTE GPPQPLSAEE KKEIDKRSVY VGNVDYGSTA QDLEAHFSSC GSINRITILC DKFSGHPKGY AYIEFAERNS VDAAVAMDET VFRGRTIKVL PKRTNMPGIS STDR

Total weight

27066.2 Da

Max. entity weight

13533.1 Da

Source organism

Xenopus laevis

Exptl. method

solution NMR

Refine. method

Torsion Angle Dynamics, Simulated Annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.8 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.8 % (1184 of 1380)	83.7 % (599 of 716)	85.9 % (464 of 540)	97.6 % (121 of 124)
Backbone	97.1 % (709 of 730)	95.6 % (239 of 250)	97.5 % (354 of 363)	99.1 % (116 of 117)
Sidechain	77.0 % (589 of 765)	77.3 % (360 of 466)	76.7 % (224 of 292)	71.4 % (5 of 7)
Aromatic	46.7 % (43 of 92)	76.1 % (35 of 46)	17.4 % (8 of 46)
Methyl	90.0 % (108 of 120)	88.3 % (53 of 60)	91.7 % (55 of 60)

1. ePABP2-trp

AIAPCMQTTH SKMTAGAYTE GPPQPLSAEE KKEIDKRSVY VGNVDYGSTA QDLEAHFSSC GSINRITILC DKFSGHPKGY AYIEFAERNS VDAAVAMDET VFRGRTIKVL PKRTNMPGIS STDR

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

Sample #2

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O,10% D2O,0.5 mM 13C,15N-ePABP2-trp, 0.5 mM Unlabeled ePABP2-trp

#	Name	Isotope labeling	Concentration
4	ePABP2-trp	[U-100% 13C; U-100% 15N]	0.5 mM
5	ePABP2-trp	natural abundance	0.5 mM
6	NaCl	natural abundance	100 mM
7	NaAc	natural abundance	10 mM

Sample #3

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 5% PEG, 10 mM sodium acetate, 100 mM NaCl, 90% H2O, 10% D2O, 0.5 mM 15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
8	ePABP2-trp	[U-100% 15N]	0.5 mM
9	PEG	natural abundance	5 %
10	NaCl	natural abundance	100 mM
11	NaAc	natural abundance	10 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.21 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.21 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JWN, Strand ID: A, B Detail

Release date

2007-10-18

Citation

Structural basis for RNA recognition by a type II poly(A)-binding protein
Song, J., McGivern, J.V., Nichols, K.W., Markley, J.L., Sheets, M.D.
Proc. Natl. Acad. Sci. U. S. A. (2008), 105, 15317-15322, PubMed 18824697 , DOI 10.1073/pnas.0801274105 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: Q6TY21 released on 2006-06-13
Title EPA2B_XENLA Entity Embryonic polyadenylate-binding protein 2-B

Related entities 1. ePABP2-trp, : 1 : 1 : 45 entities Detail

Experiments performed 13 experiments Detail

1 1H,15N-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

2 1H,13C-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

3 HNCACB

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

4 HCCONH

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

5 CBCACONH

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

6 CCONH

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

7 HCCHTOCSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

8 HBACONH

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

9 13C-EDITED 1H,1H-NOESY (aliph)

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

10 15N-EDITED 1H,1H-NOESY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

11 13C,15N filtered, 13C EDITED 1H,1H-NOESY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O,10% D2O,0.5 mM 13C,15N-ePABP2-trp, 0.5 mM Unlabeled ePABP2-trp

#	Name	Isotope labeling	Concentration
4	ePABP2-trp	[U-100% 13C; U-100% 15N]	0.5 mM
5	ePABP2-trp	natural abundance	0.5 mM
6	NaCl	natural abundance	100 mM
7	NaAc	natural abundance	10 mM

12 15N IPAP HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State anisotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 302 K, pH 5.0, Details 5% PEG, 10 mM sodium acetate, 100 mM NaCl, 90% H2O, 10% D2O, 0.5 mM 15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
8	ePABP2-trp	[U-100% 15N]	0.5 mM
9	PEG	natural abundance	5 %
10	NaCl	natural abundance	100 mM
11	NaAc	natural abundance	10 mM

13 13C-EDITED 1H,1H-NOESY (arom)

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0, Details 10 mM sodium acetate, 100 mM NaCl,90% H2O, 10% D2O,1.0 mM 13,15N-ePABP2-trp

#	Name	Isotope labeling	Concentration
1	ePABP2-trp	[U-100% 13C; U-100% 15N]	1 mM
2	NaCl	natural abundance	100 mM
3	NaAc	natural abundance	10 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15528_2jwn.nef
Input source #2: Coordindates	2jwn.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDET
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDET

-------110-------120----
VFRGRTIKVLPKRTNMPGISSTDR
||||||||||||||||||||||||
VFRGRTIKVLPKRTNMPGISSTDR

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDET
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDET

-------110-------120----
VFRGRTIKVLPKRTNMPGISSTDR
||||||||||||||||||||||||
VFRGRTIKVLPKRTNMPGISSTDR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	124	0	0	100.0
B	B	124	0	0	100.0

Content subtype: combined_15528_2jwn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1189		100.0 (chain: A, length: 124)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	4244 (1)	undefined	98.4 (chain: A, length: 124), 98.4 (chain: B, length: 124)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	56 (1)	hbond	33.9 (chain: A, length: 124), 33.9 (chain: B, length: 124)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	254 (254)	.	72.6 (chain: A, length: 124), 72.6 (chain: B, length: 124)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	177 (177)	.	71.8 (chain: A, length: 124), 70.2 (chain: B, length: 124)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 605
  - ¹³C chemical shifts: 460
  - ¹⁵N chemical shifts: 124
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
37	ARG	HH11	6.616
103	ARG	HH11	6.555

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	716	603	84.2
¹³C chemical shifts	540	460	85.2
¹⁵N chemical shifts	131	124	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	250	243	97.2
¹³C chemical shifts	248	238	96.0
¹⁵N chemical shifts	117	116	99.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	466	360	77.3
¹³C chemical shifts	292	222	76.0
¹⁵N chemical shifts	14	8	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	55	85.9
¹³C chemical shifts	64	54	84.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	34	73.9
¹³C chemical shifts	46	8	17.4

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 98.4%
  - Entity_assembly_ID: B, Chain length: 124, Sequence coverage: 98.4%
- Total number of restraints: 4243
- Weight of restraints: 1.0 (4243)
- Potential type of restraints: square-well-parabolic (4243)
- Range of distance target values: 1.2, 2.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 33.9%
    - Entity_assembly_ID: B, Chain length: 124, Sequence coverage: 33.9%
  - Total number of restraints: 56
  - Weight of restraints: 1.0 (56)
  - Potential type of restraints: square-well-parabolic (56)
  - Range of distance target values: 1.7, 1.7 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 72.6%
  - Entity_assembly_ID: B, Chain length: 124, Sequence coverage: 72.6%
- Total number of restraints: 254
- Total number of restraints per polymer type: 254
- Weight of restraints: 1.0 (254)
- Potential type of restraints: square-well-parabolic (254)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 71.8%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDET
                  |||  | ||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||
..................TEG..Q.LSAEEKKEIDKRSVYVGNVDY.STAQDLEAHFSSCGSINRITILCDKFSGH.KGYAYIEFAERNSVDAAVAMDET
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120----
VFRGRTIKVLPKRTNMPGISSTDR
|||||||||| ||           
VFRGRTIKVL.KR           
-------110---

Entity_assembly_ID: B, Chain length: 124, Sequence coverage: 70.2%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDET
                  |||  | ||| ||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||||||||||||||||||
..................TEG..Q.LSA.EKKEIDKRSVYVGNVDY.STAQD.EAHFSSCGSINRITILCDKFSGH.KGYAYIEFAERNSVDAAVAMDET
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120----
VFRGRTIKVLPKRTNMPGISSTDR
|||||||||| ||           
VFRGRTIKVL.KR           
-------110---

Total number of restraints: 177
Potential type of restraints: undefined (177)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None

Keywords Center for Eukaryotic Structural Genomics, ePABP2, poly(A) binding, Protein Structure Initiative, PSI, Structural Genomics

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Found 1 Document (1.15 seconds)

BMRB: 15528

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. ePABP2-trp, : 1 : 1 : 45 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 6 contents Detail