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Found 1 Document (0.937 seconds)

BMRB: 15950

2K8I

solution structure of E.Coli SlyD

Authors

Weininger, U., Balbach, J.

Assembly

E.Coli SlyD

Entity

1. E.Coli SlyD (polymer, Thiol state: not present), 171 monomers, 18819.43 Da Detail

MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET DQGPVPVEIT AVEDDHVVVD GNHMLAGQNL KFNVEVVAIR EATEEELAHG HVHGAHDHHH DHDHDHHHHH H

Formula weight

18819.43 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 93.4 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.4 % (1744 of 1867)	94.3 % (894 of 948)	91.6 % (680 of 742)	96.0 % (170 of 177)
Backbone	96.0 % (975 of 1016)	96.0 % (338 of 352)	96.0 % (478 of 498)	95.8 % (159 of 166)
Sidechain	91.5 % (921 of 1007)	93.3 % (556 of 596)	88.5 % (354 of 400)	100.0 % (11 of 11)
Aromatic	57.9 % (88 of 152)	68.4 % (52 of 76)	47.4 % (36 of 76)
Methyl	98.5 % (203 of 206)	99.0 % (102 of 103)	98.1 % (101 of 103)

1. METHIONINE

MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET DQGPVPVEIT AVEDDHVVVD GNHMLAGQNL KFNVEVVAIR EATEEELAHG HVHGAHDHHH DHDHDHHHHH H

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_2	[U-13C; U-15N]		1 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: -0.24 ppm, Outliers: 2 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: -0.24 ppm, Outliers: 2 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: 0.1 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: 0.3 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2K8I, Strand ID: A Detail

Release date

2009-04-01

Citation

NMR solution structure of SlyD from Escherichia coli: spatial separation of prolyl isomerase and chaperone function
Weininger, U., Haupt, C., Schweimer, K., Graubner, W., Kovermann, M., Bruser, T., Scholz, C., Schaarschmidt, P., Zoldak, G., Schmid, F.X., Balbach, J.
J. Mol. Biol. (2009), 387, 295-305, PubMed 19356587 , DOI 10.1016/j.jmb.2009.01.034 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P0A9K9 released on 2005-07-19
Title SLYD_ECOLI Entity FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

Related entities 1. E.Coli SlyD, : 1 : 5 : 26 entities Detail

Experiments performed 9 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15950_2k8i.nef
Input source #2: Coordindates	2k8i.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
MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRFLAET
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRFLAET

-------110-------120-------130-------140-------150-------160-------170-
DQGPVPVEITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIREATEEELAHGHVHGAHDHHHDHDHDHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DQGPVPVEITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIREATEEELAHGHVHGAHDHHHDHDHDHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	171	0	0	100.0

Content subtype: combined_15950_2k8i.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1736		97.1 (chain: A, length: 171)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	5001 (1)	noe	96.5 (chain: A, length: 171)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	258 (258)	.	86.5 (chain: A, length: 171)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	76 (76)	.	44.4 (chain: A, length: 171)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 171, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 892
  - ¹³C chemical shifts: 676
  - ¹⁵N chemical shifts: 168
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	948	892	94.1
¹³C chemical shifts	742	676	91.1
¹⁵N chemical shifts	181	168	92.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	352	338	96.0
¹³C chemical shifts	342	323	94.4
¹⁵N chemical shifts	166	157	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	596	554	93.0
¹³C chemical shifts	400	353	88.2
¹⁵N chemical shifts	15	11	73.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	106	99.1
¹³C chemical shifts	107	105	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	52	68.4
¹³C chemical shifts	76	36	47.4

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 171, Sequence coverage: 96.5%
- Total number of restraints: 5001
- Weight of restraints: 1.0 (5001)
- Potential type of restraints: square-well-parabolic (5001)
- Range of distance target values: 1.53, 6.04 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 171, Sequence coverage: 86.5%
- Total number of restraints: 258
- Total number of restraints per polymer type: 258
- Weight of restraints: 1.0 (258)
- Potential type of restraints: square-well-parabolic (258)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 171, Sequence coverage: 44.4%
- Total number of restraints: 76
- Potential type of restraints: undefined (76)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords chaperone, PPIase

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Found 1 Document (0.937 seconds)

BMRB: 15950

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. E.Coli SlyD, : 1 : 5 : 26 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail