7BMF | pdb_00007bmf

Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus in complex with dCTP

PDB DOI: https://doi.org/10.2210/pdb7BMF/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-01-20 Released: 2022-08-03
Deposition Author(s): De March, M., Onesti, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.299 (Depositor), 0.258 (DCC)
R-Value Work:
0.254 (Depositor), 0.263 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus

De March, M., Onesti, S.

To be published.

Macromolecule Content

Total Structure Weight: 103.53 kDa
Atom Count: 6,799
Modeled Residue Count: 888
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved protein	A, B	464	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0 Gene Names: MTH_1422
UniProt
Find proteins for O27473 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O27473 Go to UniProtKB: O27473
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O27473
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP (Subject of Investigation/LOI) Query on CTP Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain E [auth A]	E [auth A], O [auth B]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain O [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A], L [auth A], R [auth B], S [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B]
NO3 (Subject of Investigation/LOI) Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] P [auth B] F [auth A], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], M [auth B], N [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B]