BMRBj - BMREntryMaster

Found 1 Document (0.827 seconds)

BMRB: 15701

2K2D

solution struture of human C-terminal domain of pirh2/Northeast Structural Genomics Consortium (NESG) target HT2C

Authors

Lemak, A., Sheng, Y., Karra, M., Srisailam, S., Laister, R., Duan, S., Arrowsmith, C.

Assembly

human C-termal doamin of pirh2

Entity

1. human C-termal doamin of pirh2 (polymer, Thiol state: all other bound), 79 monomers, 9028.129 Da Detail

GSHMMHSALD MTRYWRQLDD EVAQTPMPSE YQNMTVDILC NDCNGRSTVQ FHILGMKCKI CESYNTAQAG GRRISLDQQ

2. ZN (non-polymer), 65.409 Da

Total weight

9093.538 Da

Max. entity weight

9028.129 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS40:SG	2:ZN1:ZN
2	disulfide	sing	1:CYS43:SG	2:ZN1:ZN
3	disulfide	sing	1:CYS58:SG	2:ZN1:ZN
4	disulfide	sing	1:CYS61:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 89.6 %, Completeness (bb): 88.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.6 % (805 of 898)	90.0 % (422 of 469)	91.2 % (310 of 340)	82.0 % (73 of 89)
Backbone	88.9 % (418 of 470)	88.8 % (143 of 161)	90.9 % (211 of 232)	83.1 % (64 of 77)
Sidechain	91.2 % (458 of 502)	90.6 % (279 of 308)	93.4 % (170 of 182)	75.0 % (9 of 12)
Aromatic	84.5 % (49 of 58)	82.8 % (24 of 29)	85.7 % (24 of 28)	100.0 % (1 of 1)
Methyl	97.0 % (64 of 66)	97.0 % (32 of 33)	97.0 % (32 of 33)

1. human C-termal doamin of pirh2

GSHMMHSALD MTRYWRQLDD EVAQTPMPSE YQNMTVDILC NDCNGRSTVQ FHILGMKCKI CESYNTAQAG GRRISLDQQ

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
7	sodium phosphate	natural abundance	50 mM
8	potassium chloride	natural abundance	150 mM
9	ZnCl2	natural abundance	10 uM
10	DTT	natural abundance	0.8 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: -0.09 ppm, Outliers: 1 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: -0.09 ppm, Outliers: 1 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: 0.03 ppm, Outliers: 2 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: 3.07 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2K2D, Strand ID: A Detail

Release date

2008-04-06

Citation

Molecular basis of Pirh2-mediated p53 ubiquitylation
Sheng, Y., Laister, R.C., Lemak, A., Wu, B., Tai, E., Duan, S., Lukin, J., Sunnerhagen, M., Srisailam, S., Karra, M., Benchimol, S., Arrowsmith, C.H.
Nat. Struct. Mol. Biol. (2008), 15, 1334-1342, PubMed 19043414 , DOI 10.1038/nsmb.1521 , Abstract

Related entities 1. human C-termal doamin of pirh2, : 1 : 2 : 18 entities Detail

Interaction partners 1. human C-termal doamin of pirh2, : 31 interactors Detail

More details for 31 interactors identified by 9 citations

Experiments performed 11 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

2 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

5 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

6 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
7	sodium phosphate	natural abundance	50 mM
8	potassium chloride	natural abundance	150 mM
9	ZnCl2	natural abundance	10 uM
10	DTT	natural abundance	0.8 mM

8 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
7	sodium phosphate	natural abundance	50 mM
8	potassium chloride	natural abundance	150 mM
9	ZnCl2	natural abundance	10 uM
10	DTT	natural abundance	0.8 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

11 3D 1H-13C-Aromatic NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	human C-termal doamin of pirh2	[U-99% 13C; U-99% 15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	potassium chloride	natural abundance	150 mM
4	ZnCl2	natural abundance	10 uM
5	DTT	natural abundance	0.8 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15701_2k2d.nef
Input source #2: Coordindates	2k2d.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:40:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:43:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:58:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:61:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70---------
GSHMMHSALDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQAGGRRISLDQQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMMHSALDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQAGGRRISLDQQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0

Content subtype: combined_15701_2k2d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	807		97.5 (chain: A, length: 79)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1300 (1)	noe	92.4 (chain: A, length: 79)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	8 (1)	hbond	7.6 (chain: A, length: 79)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	56 (56)	.	59.5 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 97.5%
- Total number of assignments
  - ¹H chemical shifts: 427
  - ¹³C chemical shifts: 308
  - ¹⁵N chemical shifts: 72
- 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	469	427	91.0
¹³C chemical shifts	340	308	90.6
¹⁵N chemical shifts	94	72	76.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	144	89.4
¹³C chemical shifts	158	138	87.3
¹⁵N chemical shifts	77	63	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	308	283	91.9
¹³C chemical shifts	182	170	93.4
¹⁵N chemical shifts	17	9	52.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	35	89.7
¹³C chemical shifts	39	35	89.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	26	89.7
¹³C chemical shifts	28	24	85.7
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 92.4%
- Total number of restraints: 1300
- Weight of restraints: 1.0 (1300)
- Potential type of restraints: square-well-parabolic (1300)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 7.6%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: square-well-parabolic (8)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 59.5%
- Total number of restraints: 56
- Total number of restraints per polymer type: 56
- Weight of restraints: 1.0 (56)
- Potential type of restraints: square-well-parabolic (56)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords zinc-binding protein

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 (0.827 seconds)

BMRB: 15701

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. human C-termal doamin of pirh2, : 1 : 2 : 18 entities Detail

Interaction partners 1. human C-termal doamin of pirh2, : 31 interactors Detail

Experiments performed 11 experiments Detail

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