3DM3 | pdb_00003dm3

Crystal structure of a domain of a Replication factor A protein, from Methanocaldococcus jannaschii. NorthEast Structural Genomics target MjR118E

PDB DOI: https://doi.org/10.2210/pdb3DM3/pdb

Classification: REPLICATION
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-30 Released: 2008-08-26
Deposition Author(s): Seetharaman, J., Su, M., Maglaqui, M., Janjua, H., Ciccosanti, C., Xiao, R., Nair, R., Everett, J.K., 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: 2.40 Å
R-Value Free:
0.274 (Depositor), 0.282 (DCC)
R-Value Work:
0.225 (Depositor), 0.235 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a domain of a Replication factor A protein, from Methanocaldococcus jannaschii. NorthEast Structural Genomics target MjR118E

Seetharaman, J., Su, M., Maglaqui, M., Janjua, H., Ciccosanti, C., Xiao, R., Nair, R., Everett, J.K., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 35.3 kDa
Atom Count: 2,492
Modeled Residue Count: 294
Deposited Residue Count: 315
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor A	A, B, C	105	Methanocaldococcus jannaschii	Mutation(s): 0 Gene Names: rpa, MJ1159
UniProt
Find proteins for Q58559 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58559 Go to UniProtKB: Q58559
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58559
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.274 (Depositor), 0.282 (DCC)
R-Value Work: 0.225 (Depositor), 0.235 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.001	α = 90
b = 76.001	β = 90
c = 249.479	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations