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- PDB-3f6s: Desulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin alte... -

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Basic information

Entry
Database: PDB / ID: 3f6s
TitleDesulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin alternate conformers
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 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 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Oct 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 1.6Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavodoxin
B: Flavodoxin
D: Flavodoxin
E: Flavodoxin
F: Flavodoxin
H: Flavodoxin
I: Flavodoxin
G: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,30216
Polymers125,6518
Non-polymers3,6518
Water5,531307
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
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
4
E: 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
5
F: 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
6
H: 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
7
I: 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
8
G: 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)94.89, 94.89, 238.1
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 62:67 )
211chain A and (resseq 62:67 )
311chain G and (resseq 62:67 )
411chain E and (resseq 62:67 )

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Components

#1: Protein
Flavodoxin /


Mass: 15706.387 Da / Num. of mol.: 8 / 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 / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M potassium thiocyanate, 2.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 4, 2008
RadiationMonochromator: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.071
11-h,-k,l20.929
ReflectionResolution: 2.5→20 Å / Num. obs: 43662 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 10.4 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 8 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 9.8 / Num. unique all: 6303 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
PHASERphasing
CNSrefinement
JBluIce-EPICSGUI: Blu Ice processingdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Desulfovibrio desulfuricans flavodoxin solved in alternate space group

Resolution: 2.502→19.889 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 2.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 4386 10.06 %random
Rwork0.2198 ---
obs0.2258 43606 99.78 %-
all-43606 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.067 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso mean: 67.14 Å2
Baniso -1Baniso -2Baniso -3
1--48.88 Å20 Å2-0 Å2
2---48.88 Å2-0 Å2
3----53.88 Å2
Refinement stepCycle: LAST / Resolution: 2.502→19.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8744 0 248 307 9299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.01
X-RAY DIFFRACTIONf_bond_d0.006
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B50X-RAY DIFFRACTIONPOSITIONAL
12A50X-RAY DIFFRACTIONPOSITIONAL0.03
13G50X-RAY DIFFRACTIONPOSITIONAL0.032
14E50X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.502-2.54460.37252080.240218262034
2.5446-2.59080.29452210.243619182139
2.5908-2.64050.31212120.244619702182
2.6405-2.69430.3022240.233519302154
2.6943-2.75270.34492150.234619152130
2.7527-2.81660.27992230.232219332156
2.8166-2.88680.32662210.235619372158
2.8868-2.96460.29842140.223619582172
2.9646-3.05160.30352150.221419642179
3.0516-3.14970.29212340.229219192153
3.1497-3.26180.24391970.226619812178
3.2618-3.39180.28142020.206419722174
3.3918-3.54530.27042140.204619422156
3.5453-3.73110.25052330.207619592192
3.7311-3.96310.24332190.19119782197
3.9631-4.26630.23372300.182819682198
4.2663-4.69060.21392320.179619712203
4.6906-5.35770.27272260.205219992225
5.3577-6.70680.32632220.280720412263
6.7068-19.88990.27432240.261421392363

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