2ARK | pdb_00002ark

Structure of a flavodoxin from Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb2ARK/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Aquifex aeolicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-08-19 Released: 2005-10-25
Deposition Author(s): Cuff, M.E., Quartey, P., Zhou, M., Cymborowski, M., Minor, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.235 (Depositor), 0.230 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of a flavodoxin from Aquifex aeolicus

Cuff, M.E., Quartey, P., Zhou, M., Cymborowski, M., Minor, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 127.56 kDa
Atom Count: 9,119
Modeled Residue Count: 1,116
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavodoxin	A, B, C, D, E A, B, C, D, E, F	188	Aquifex aeolicus	Mutation(s): 7 Gene Names: fldA, floX
UniProt
Find proteins for O67866 (Aquifex aeolicus (strain VF5)) Explore O67866 Go to UniProtKB: O67866
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O67866
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain O [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain O [auth D]	G [auth A] J [auth B] L [auth C] O [auth D] Q [auth E] G [auth A], J [auth B], L [auth C], O [auth D], Q [auth E], R [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain N [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C]	H [auth A] I [auth A] K [auth B] M [auth C] N [auth C] H [auth A], I [auth A], K [auth B], M [auth C], N [auth C], P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.235 (Depositor), 0.230 (DCC)
R-Value Work: 0.171 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.846	α = 90
b = 112.846	β = 90
c = 150.648	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELX	phasing
RESOLVE	phasing
DM	phasing
Coot	model building
O	model building
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-10-25

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-10-25
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-11-13
Changes: Data collection, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 2ARK | pdb_00002ark

Structure of a flavodoxin from Aquifex aeolicus

Structure of a flavodoxin from Aquifex aeolicus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

2ARK | pdb_00002ark