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- PDB-3kaq: Flavodoxin from D. desulfuricans (semireduced form) -

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Basic information

Entry
Database: PDB / ID: 3kaq
TitleFlavodoxin from D. desulfuricans (semireduced form)
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / flavodoxin / sulfate-reducing bacteria / Flavoprotein / FMN / Transport
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRomero, A. / Caldeira, J. / LeGall, J. / Moura, I. / Moura, J.J.G. / Romao, M.J.
CitationJournal: Eur.J.Biochem. / Year: 1996
Title: Crystal structure of flavodoxin from Desulfovibrio desulfuricans ATCC 27774 in two oxidation states.
Authors: Romero, A. / Caldeira, J. / Legall, J. / Moura, I. / Moura, J.J. / Romao, M.J.
History
DepositionOct 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9042
Polymers15,4471
Non-polymers4561
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.100, 95.100, 33.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Flavodoxin


Mass: 15447.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 (bacteria)
Strain: ATCC 27774 / DSM 6949 / References: UniProt: P80312
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Reduced flavodoxin crystals were obtained directly from the oxidized ones. Since the original conditions of growth were at pH=5.0, the crystals were carefully transferred to 2.5M ammonium ...Details: Reduced flavodoxin crystals were obtained directly from the oxidized ones. Since the original conditions of growth were at pH=5.0, the crystals were carefully transferred to 2.5M ammonium sulfate, pH=7.0, the pH required for the reduction to the semiquinone state. Within 10-15 min of 100mM sodium dithionite being slowly added, the crystal colour gradually changed from yellow to purple, corresponding to the stable semireduced state., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→24 Å / Num. all: 10220 / Num. obs: 9173 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.155
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.367 / % possible all: 93.3

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Processing

Software
NameVersionClassification
MAR345data collection
X-PLORmodel building
X-PLOR3.1refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KAP

3kap


Resolution: 2.25→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rwork0.194 -
obs0.194 8738
Rfree-0
all-9112
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 31 83 1181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg2.981
X-RAY DIFFRACTIONx_dihedral_angle_d26.06
X-RAY DIFFRACTIONx_improper_angle_d2.38
LS refinement shellResolution: 2.15→2.25 Å /
RfactorNum. reflection
Rwork0.275 -
Rfree-0
obs-1117

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