3PFI | pdb_00003pfi

2.7 Angstrom resolution crystal structure of a probable holliday junction DNA helicase (ruvB) from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with adenosine-5'-diphosphate

PDB DOI: https://doi.org/10.2210/pdb3PFI/pdb

Classification: HYDROLASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-10-28 Released: 2010-11-10
Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Skarina, T., Onopriyenko, O., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.268 (Depositor), 0.280 (DCC)
R-Value Work:
0.222 (Depositor), 0.235 (DCC)
R-Value Observed:
0.224 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

2.7 Angstrom resolution crystal structure of a probable holliday junction DNA helicase (ruvB) from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with adenosine-5'-diphosphate

Halavaty, A.S., Wawrzak, Z., Skarina, T., Onopriyenko, O., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 76.77 kDa
Atom Count: 4,636
Modeled Residue Count: 584
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction ATP-dependent DNA helicase ruvB	A, B	338	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0 Gene Names: CJJ8425_1444, ruvB EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for Q9PMT7 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PMT7 Go to UniProtKB: Q9PMT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PMT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 2.69 Å
R-Value Free: 0.268 (Depositor), 0.280 (DCC)
R-Value Work: 0.222 (Depositor), 0.235 (DCC)
R-Value Observed: 0.224 (Depositor)

Diffraction Data:

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.482	α = 90
b = 111.482	β = 90
c = 355.089	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-11-10

Deposition Author(s):

Onopriyenko, O.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.