2O1M

Crystal structure of the probable amino-acid ABC transporter extracellular-binding protein ytmK from Bacillus subtilis. Northeast Structural Genomics Consortium target SR572

PDB DOI: https://doi.org/10.2210/pdb2O1M/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-11-29 Released: 2006-12-19
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Chen, C.X., Fang, Y., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.230
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the probable amino-acid ABC transporter extracellular-binding protein ytmK from Bacillus subtilis. Northeast Structural Genomics Consortium target SR572.

Kuzin, A.P., Su, M., Seetharaman, J., Chen, C., Fang, Y., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 59.18 kDa
Atom Count: 3,969
Modelled Residue Count: 456
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable amino-acid ABC transporter extracellular-binding protein ytmK	A, B	258	Bacillus subtilis	Mutation(s): 3 Gene Names: ytmK
UniProt
Find proteins for O34852 (Bacillus subtilis (strain 168)) Explore O34852 Go to UniProtKB: O34852
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34852
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	C [auth A], D [auth A], E [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.230
R-Value Observed: 0.230
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.563	α = 90
b = 88.931	β = 90
c = 76.697	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-12-19

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-12-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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2O1M

Crystal structure of the probable amino-acid ABC transporter extracellular-binding protein ytmK from Bacillus subtilis. Northeast Structural Genomics Consortium target SR572

Crystal structure of the probable amino-acid ABC transporter extracellular-binding protein ytmK from Bacillus subtilis. Northeast Structural Genomics Consortium target SR572.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)