8Q67 | pdb_00008q67

Crystal structure of a homohexameric MCM from M. acidophilum

PDB DOI: https://doi.org/10.2210/pdb8Q67/pdb

Classification: REPLICATION
Organism(s): Candidatus Mancarchaeum acidiphilum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-08-11 Released: 2025-03-12
Deposition Author(s): Noble, O.W., Degut, C., Hodgkinson, M.R., Chong, J.P.J., Plevin, M.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.253 (Depositor), 0.254 (DCC)
R-Value Work:
0.231 (Depositor), 0.231 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Fundamental steps of Minichromosome Maintenance complex assembly are conserved from archaea to eukaryotes

Noble, O.W., Degut, C., Hodgkinson, M.R., Chong, J.P.J., Plevin, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 401.87 kDa
Atom Count: 27,120
Modeled Residue Count: 3,453
Deposited Residue Count: 3,606
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase	A, B, C, D, E A, B, C, D, E, F	601	Candidatus Mancarchaeum acidiphilum	Mutation(s): 1 Gene Names: Mia14_0611 EC: 3.6.4.12
UniProt
Find proteins for A0A218NN99 (Candidatus Mancarchaeum acidiphilum) Explore A0A218NN99 Go to UniProtKB: A0A218NN99
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A218NN99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain S [auth E] SDF format, chain V [auth F] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F] mmCIF format, chain J [auth B]	G [auth A], J [auth B], M [auth C], S [auth E], V [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain S [auth E] Focus chain V [auth F]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain W [auth F] SDF format, chain T [auth E] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain W [auth F] MOL2 format, chain T [auth E] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain W [auth F] mmCIF format, chain T [auth E]	H [auth A] K [auth B] N [auth C] P [auth D] Q [auth D] H [auth A], K [auth B], N [auth C], P [auth D], Q [auth D], T [auth E], W [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F]	I [auth A] L [auth B] O [auth C] R [auth D] U [auth E] I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.253 (Depositor), 0.254 (DCC)
R-Value Work: 0.231 (Depositor), 0.231 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 228.699	α = 90
b = 127.488	β = 91.713
c = 177.038	γ = 90

Software Package:

Software Name	Purpose
X-Area	data reduction
DIALS	data scaling
PHASER	phasing
Coot	model building
BUCCANEER	model building
PHENIX	model building
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L013770/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M015831/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/S506795/1