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BMRB: 17002

2KZC

Solution NMR structure of the protein YP_510488.1

Authors

MOHANTY, B., SERRANO, P., GERALT, M., HORST, R., WILSON, I.A., WUTHRICH, K.

Assembly

YP 510488.1

Entity

1. YP 510488.1 (polymer, Thiol state: not present), 85 monomers, 9353.582 Da Detail

GMQFKAEARR NKLMGLWVAE VLGKSGDEAN AYAAEVVKAD FEEAGHEDVM RKVLGDLDGK RPEAEVRAKY EGLMAVAKAQ LMDEL

Formula weight

9353.582 Da

Source organism

Jannaschia sp. CCS1

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.4 %, Completeness (bb): 96.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.4 % (936 of 961)	99.2 % (497 of 501)	95.1 % (353 of 371)	96.6 % (86 of 89)
Backbone	96.1 % (488 of 508)	97.7 % (173 of 177)	95.1 % (235 of 247)	95.2 % (80 of 84)
Sidechain	97.5 % (517 of 530)	99.1 % (321 of 324)	95.0 % (191 of 201)	100.0 % (5 of 5)
Aromatic	80.8 % (42 of 52)	96.2 % (25 of 26)	64.0 % (16 of 25)	100.0 % (1 of 1)
Methyl	97.8 % (90 of 92)	97.8 % (45 of 46)	97.8 % (45 of 46)

1. entity

GMQFKAEARR NKLMGLWVAE VLGKSGDEAN AYAAEVVKAD FEEAGHEDVM RKVLGDLDGK RPEAEVRAKY EGLMAVAKAQ LMDEL

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.27 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.27 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.18 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.53 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2010-09-01

Citation

Solution NMR structure of the protein YP_510488.1
MOHANTY, B., SERRANO, P., GERALT, M., HORST, R., WILSON, I.A., WUTHRICH, K.
Not known

Related entities 1. YP 510488.1, : 1 : 5 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 4D APSY - HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 5D APSY - HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 5D APSY - CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 15N Resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 13Cali Resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 13Caro Resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details PC07345C, NaCl, Na2PO4, NaN3

#	Name	Isotope labeling	Type	Concentration
1	PC07345C	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17002_2kzc.nef
Input source #2: Coordindates	2kzc.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-----
GMQFKAEARRNKLMGLWVAEVLGKSGDEANAYAAEVVKADFEEAGHEDVMRKVLGDLDGKRPEAEVRAKYEGLMAVAKAQLMDEL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMQFKAEARRNKLMGLWVAEVLGKSGDEANAYAAEVVKADFEEAGHEDVMRKVLGDLDGKRPEAEVRAKYEGLMAVAKAQLMDEL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_17002_2kzc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	935		98.8 (chain: A, length: 85)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1667 (1)	noe	98.8 (chain: A, length: 85)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	310 (309)	.	100.0 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 98.8%
- Total number of assignments
  - ¹H chemical shifts: 493
  - ¹³C chemical shifts: 352
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 98.8%
- Total number of restraints: 1667
- Weight of restraints: 1.0 (1667)
- Potential type of restraints: upper-bound-parabolic (1667)
- Range of distance target values: 2.4, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 100.0%
- Total number of restraints: 309
- Total number of restraints per polymer type: 309
- Weight of restraints: 1.0 (309)
- Potential type of restraints: square-well-parabolic (309)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DUF1476, JANNASCHIA SP. strain CCS1, JCSG, Protein Structure initiative, PSI2, Structutral genomics, YP_510488.1