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- PDB-3f6r: Desulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin -

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Basic information

Entry
Database: PDB / ID: 3f6r
TitleDesulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / flavodoxin-like fold / FMN binding / oxidized / 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 ...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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuelker, M. / Shamoo, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin.
Authors: Guelker, M. / Stagg, L. / Wittung-Stafshede, P. / Shamoo, Y.
History
DepositionNov 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Aug 14, 2019Group: Data collection / Category: computing
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin
B: Flavodoxin
C: Flavodoxin
D: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6518
Polymers62,8264
Non-polymers1,8254
Water6,179343
1
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1632
Polymers15,7061
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1632
Polymers15,7061
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1632
Polymers15,7061
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1632
Polymers15,7061
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.06, 71.06, 112.99
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Flavodoxin


Mass: 15706.387 Da / Num. of mol.: 4 / Mutation: N79D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Strain: ATCC 29577 / Gene: flavodoxin / Plasmid: pET-24c(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P26492
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1M sodium citrate, 2.4M ammonium sulfate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 10, 2008 / Details: Rigaku Varimax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.475
ReflectionResolution: 1.97→37.53 Å / Num. all: 39723 / Num. obs: 29589 / % possible obs: 74.5 % / Observed criterion σ(I): 3 / Redundancy: 5.39 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.9
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3929 / % possible all: 14.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
PHASERphasing
CNSrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AZL with side chains pruned to the last common atom

1azl


Resolution: 2→37.53 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 1.94 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 2976 10.11 %random
Rwork0.2112 ---
obs0.215 29422 77.72 %-
all-29422 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.615 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 33.46 Å2
Baniso -1Baniso -2Baniso -3
1--7.58 Å2-7.58 Å2-0 Å2
2---0 Å2-7.58 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 124 343 4839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.944
X-RAY DIFFRACTIONf_bond_d0.005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2-2.04680.2981620.286503565
2.0468-2.0980.2982960.2545766862
2.098-2.15470.28251060.2389691075
2.1547-2.21810.28731270.238211511278
2.2181-2.28970.24091420.224813631505
2.2897-2.37150.26751850.223616151800
2.3715-2.46640.26182200.213220672287
2.4664-2.57870.27922530.222621902443
2.5787-2.71460.27222390.223222732512
2.7146-2.88460.25522420.214422292471
2.8846-3.10720.25622620.213122452507
3.1072-3.41970.22872630.19822472510
3.4197-3.91410.22792270.181622752502
3.9141-4.92960.20372570.182622832540
4.9296-37.55260.27752530.242423122565

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