3F3B

Structure of the phage-like element PBSX protein xkdH from Bacillus Subtilus. Northeast Structural Genomics Consortium target SR352.

PDB DOI: https://doi.org/10.2210/pdb3F3B/pdb

Classification: structural genomics, unknown function
Organism(s): Bacillus subtilis
Mutation(s): No

Deposited: 2008-10-30 Released: 2008-11-25
Deposition Author(s): Kuzin, A.P., Neely, H., Seetharaman, J., Clayton, G., Ho, C.K., Janjua, H., 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., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.263
R-Value Work: 0.230
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the phage-like element PBSX protein xkdH from Bacillus Subtilus. Northeast Structural Genomics Consortium target SR352.

Kuzin, A.P., Neely, H., Seetharaman, J., Clayton, G., Ho, C.K., 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: 15.35 kDa
Atom Count: 1,031
Modelled Residue Count: 115
Deposited Residue Count: 126
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage-like element PBSX protein xkdH	A	126	Bacillus subtilis	Mutation(s): 0 Gene Names: xkdH, BSU12620
UniProt
Find proteins for P54328 (Bacillus subtilis (strain 168)) Explore P54328 Go to UniProtKB: P54328
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54328
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.263
R-Value Work: 0.230
R-Value Observed: 0.230
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.661	α = 90
b = 42.661	β = 90
c = 283.65	γ = 120

Software Package:

Software Name	Purpose
APEX	data collection
SnB	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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Help and Resources

3F3B

Structure of the phage-like element PBSX protein xkdH from Bacillus Subtilus. Northeast Structural Genomics Consortium target SR352.

Structure of the phage-like element PBSX protein xkdH from Bacillus Subtilus. Northeast Structural Genomics Consortium target SR352.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)