2AQP | pdb_00002aqp

CU/ZN superoxide dismutase from neisseria meningitidis E73A mutant

PDB DOI: https://doi.org/10.2210/pdb2AQP/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: 1.30 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.135 (Depositor), 0.140 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

CU/ZN superoxide dismutase from neisseria meningitidis E73A 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: 35.54 kDa
Atom Count: 2,760
Modeled Residue Count: 310
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B	164	Neisseria meningitidis	Mutation(s): 1 Gene Names: sodC EC: 1.15.1.1
UniProt
Find proteins for P57005 (Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491)) Explore P57005 Go to UniProtKB: P57005
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P57005
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 D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B]	D [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]
CU1 Query on CU1 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	C [auth A], E [auth A], L [auth B]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain L [auth B]
EDO Query on EDO 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 I [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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 J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [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 J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.135 (Depositor), 0.140 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.874	α = 90
b = 48.697	β = 109.57
c = 49.042	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-10-31

Deposition Author(s):

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: Derived calculations, 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: 2024-10-16
Changes: Structure summary