4FDB | pdb_00004fdb

Three-dimensional structure of the protein prib from ralstonia solanacearum at the resolution 1.8a. northeast structural genomics consortium target rsr213c

PDB DOI: https://doi.org/10.2210/pdb4FDB/pdb

Classification: REPLICATION
Organism(s): Ralstonia pseudosolanacearum GMI1000
Mutation(s): Yes

Deposited: 2012-05-27 Released: 2013-02-13
Deposition Author(s): Kuzin, A., Neely, H., Seetharaman, J., Wang, H., Sahdev, S., Foote, E.L., Xiao, R., Liu, J., Everett, J.K., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.217 (Depositor), 0.228 (DCC)
R-Value Work:
0.196 (Depositor), 0.202 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Three-dimensional structure of the protein prib from ralstonia solanacearum at the resolution 1.8a. northeast structural genomics consortium target rsr213c

Kuzin, A., Neely, H., Seetharaman, J., Wang, H., Sahdev, S., Foote, E.L., Xiao, R., Liu, J., Everett, J.K., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 11.28 kDa
Atom Count: 842
Modeled Residue Count: 95
Deposited Residue Count: 101
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable primosomal replication protein n	A	101	Ralstonia pseudosolanacearum GMI1000	Mutation(s): 3 Gene Names: priB, RSc1308
UniProt
Find proteins for Q8XZT7 (Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000)) Explore Q8XZT7 Go to UniProtKB: Q8XZT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8XZT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 1.80 Å
R-Value Free: 0.217 (Depositor), 0.228 (DCC)
R-Value Work: 0.196 (Depositor), 0.202 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.661	α = 90
b = 70.661	β = 90
c = 141.117	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-10-09
Changes: Structure summary