2AQR | pdb_00002aqr

CU/ZN superoxide dismutase from neisseria meningitidis K91Q mutant

PDB DOI: https://doi.org/10.2210/pdb2AQR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Neisseria meningitidis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-08-18 Released: 2006-10-31
Deposition Author(s): DiDonato, M., Kassmann, C.J., Bruns, C.K., Cabelli, D.E., Cao, Z., Tabatabai, L.B., Kroll, J.S., Getzoff, E.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.197 (Depositor), 0.193 (DCC)
R-Value Work:
0.169 (Depositor), 0.164 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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This is version 1.5 of the entry. See complete history.

Literature

CU/ZN superoxide dismutase from neisseria meningitidis K91Q mutant

DiDonato, M., Kassmann, C.J., Bruns, C.K., Cabelli, D.E., Cao, Z., Tabatabai, L.B., Kroll, J.S., Getzoff, E.D.

To be published.

Macromolecule Content

Total Structure Weight: 52.67 kDa
Atom Count: 3,926
Modeled Residue Count: 465
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B, C	164	Neisseria meningitidis	Mutation(s): 1 Gene Names: sodC EC: 1.15.1.1
UniProt
Find proteins for Q59623 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q59623 Go to UniProtKB: Q59623
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59623
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	F [auth A], H [auth B], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], J [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
CU1 Query on CU1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth C] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B]	D [auth A], G [auth B], I [auth C]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.197 (Depositor), 0.193 (DCC)
R-Value Work: 0.169 (Depositor), 0.164 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.84	α = 90
b = 65.052	β = 121.02
c = 77.443	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-10-31

Deposition Author(s):

Tabatabai, L.B.

Revision History (Full details and data files)

Version 1.0: 2006-10-31
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Data collection, Refinement description
Version 1.5: 2024-11-06
Changes: 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.