BMRBj - BMREntryMaster

Found 1 Document (0.822 seconds)

BMRB: 19013

2M4M

Solution structure of the RRM domain of the hypothetical protein CAGL0M09691g from Candida glabrata

Authors

Harris, R., Hillerich, B., Ahmed, M., Bonanno, J.B., Chamala, S., Evans, B., Lafleur, J., Hammonds, J., Washington, E., Stead, M., Love, J., Attonito, J., Seidel, R.D., Chook, Y.M., Rout, M.P., Girvin, M.E., Almo, S.C., Harris, R., Hillerich, B., Ahmed, M., Bonanno, J.B., Chamala, S., Evans, B., Lafleur, J., Washington, E., Stead, M., Love, J., Attonito, J., Patel, H., Seidel, R.D., Chook, Y.M., Rout, M.P., Girvin, M.E., Almo, S.C.

Assembly

RRM domain of the hypothetical protein

Entity

1. RRM domain of the hypothetical protein (polymer, Thiol state: all free), 124 monomers, 14204.67 Da Detail

MSLGSESETG NAVVVFGYRE AITKQILAYF AQFGEILEDL ESELGDTETM RTPGYFFQQA PNRRRISREH GRTWTKLTYA NHSSYLRALR EHGTIYCGAA IGCVPYKHEL ISELSREGHH HHHH

Formula weight

14204.67 Da

Source organism

[Candida] glabrata

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 93.2 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (1336 of 1433)	91.9 % (681 of 741)	94.0 % (529 of 563)	97.7 % (126 of 129)
Backbone	97.6 % (720 of 738)	96.5 % (247 of 256)	98.3 % (355 of 361)	97.5 % (118 of 121)
Sidechain	90.0 % (727 of 808)	89.5 % (434 of 485)	90.5 % (285 of 315)	100.0 % (8 of 8)
Aromatic	75.9 % (120 of 158)	74.7 % (59 of 79)	76.9 % (60 of 78)	100.0 % (1 of 1)
Methyl	100.0 % (120 of 120)	100.0 % (60 of 60)	100.0 % (60 of 60)

1. RRM domain of the hypothetical protein

MSLGSESETG NAVVVFGYRE AITKQILAYF AQFGEILEDL ESELGDTETM RTPGYFFQQA PNRRRISREH GRTWTKLTYA NHSSYLRALR EHGTIYCGAA IGCVPYKHEL ISELSREGHH HHHH

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
8	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
9	sodium acetate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	0.5 mM
12	EDTA	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: 0.0 ppm, Outliers: 5 Detail

LACS Plot; CB

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

Referencing offset: 0.0 ppm, Outliers: 5 Detail

LACS Plot; HA

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

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.01 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M4M, Strand ID: A Detail

Release date

2013-03-05

Related entities 1. RRM domain of the hypothetical protein, : 1 : 10 entities Detail

Experiments performed 12 experiments Detail

1 15N HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 15N NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
8	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
9	sodium acetate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	0.5 mM
12	EDTA	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

4 aromatic 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
8	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
9	sodium acetate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	0.5 mM
12	EDTA	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

5 13C NOESY-HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
8	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
9	sodium acetate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	0.5 mM
12	EDTA	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

6 13C aromatic NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
8	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
9	sodium acetate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	0.5 mM
12	EDTA	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

7 HNCO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 HNCACO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

9 HNCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

10 HNCOCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

11 HNCACB

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

12 CBCACONH

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na Acetate buffer, 100mM NaCl, pH 4.5, 0.5mM DTT, 0.5mM EDTA

#	Name	Isotope labeling	Concentration
1	RRM domain of the hypothetical protein	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	0.5 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19013_2m4m.nef
Input source #2: Coordindates	2m4m.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
MSLGSESETGNAVVVFGYREAITKQILAYFAQFGEILEDLESELGDTETMRTPGYFFQQAPNRRRISREHGRTWTKLTYANHSSYLRALREHGTIYCGAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLGSESETGNAVVVFGYREAITKQILAYFAQFGEILEDLESELGDTETMRTPGYFFQQAPNRRRISREHGRTWTKLTYANHSSYLRALREHGTIYCGAA

-------110-------120----
IGCVPYKHELISELSREGHHHHHH
||||||||||||||||||||||||
IGCVPYKHELISELSREGHHHHHH

Chain assignments

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

Content subtype: combined_19013_2m4m.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1357		99.2 (chain: A, length: 124)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1815 (1)	noe	97.6 (chain: A, length: 124)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	67 (1)	noe	35.5 (chain: A, length: 124)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	108 (108)	.	56.5 (chain: A, 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: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 694
  - ¹³C chemical shifts: 532
  - ¹⁵N chemical shifts: 131
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	741	694	93.7
¹³C chemical shifts	563	532	94.5
¹⁵N chemical shifts	139	131	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	256	250	97.7
¹³C chemical shifts	248	246	99.2
¹⁵N chemical shifts	121	117	96.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	485	444	91.5
¹³C chemical shifts	315	286	90.8
¹⁵N chemical shifts	18	14	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	61	98.4
¹³C chemical shifts	62	61	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	79	64	81.0
¹³C chemical shifts	78	63	80.8
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 97.6%
- Total number of restraints: 1810
- Weight of restraints: 1.0 (1810)
- Potential type of restraints: square-well-parabolic (1810)
- Range of distance target values: 2.4, 4.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 35.5%
  - Total number of restraints: 66
  - Weight of restraints: 1.0 (66)
  - Potential type of restraints: square-well-parabolic (66)
  - Range of distance target values: 2.4, 3.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: 56.5%
- Total number of restraints: 108
- Total number of restraints per polymer type: 108
- Weight of restraints: 1.0 (108)
- Potential type of restraints: square-well-parabolic (108)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords New York Structural Genomics Research Consortium, STRUCTURAL GENOMICS, THIOREDOXIN-LIKE, UNKNOWN FUNCTION

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.822 seconds)

BMRB: 19013

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. RRM domain of the hypothetical protein, : 1 : 10 entities Detail

Experiments performed 12 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail