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- PDB-1c7f: D95E OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS -

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Basic information

Entry
Database: PDB / ID: 1c7f
TitleD95E OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / ELECTRON TRANSFER / FLAVOPROTEIN / FMN / FLAVODOXIN / MUTANT
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-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily ...Flavodoxin, short chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / 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 vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcCarthy, A. / Walsh, M. / Higgins, T. / D'Arcy, D.
CitationJournal: Biochemistry / Year: 2002
Title: Crystallographic Investigation of the Role of Aspartate 95 in the Modulation of the Redox Potentials Of Desulfovibrio Vulgaris Flavodoxin
Authors: McCarthy, A.A. / Walsh, M.A. / Verma, C.S. / O'Connell, D.P. / Reinhold, M. / Yalloway, G.N. / D'Arcy, D. / Higgins, T.M. / Voordouw, G. / Mayhew, S.G.
History
DepositionFeb 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAVODOXIN
B: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3494
Polymers31,4362
Non-polymers9132
Water2,666148
1
A: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1752
Polymers15,7181
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1752
Polymers15,7181
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.315, 61.933, 77.421
Angle α, β, γ (deg.)90.00, 127.16, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.40173, -0.91575, -0.0048), (0.91571, -0.40164, -0.01274), (0.00974, -0.00952, 0.99991)
Vector: 9.00876, -7.51871, 38.8879)

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Components

#1: Protein FLAVODOXIN


Mass: 15718.172 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: TG2 / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TG2 / References: UniProt: P00323
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.09 Å3/Da / Density % sol: 59.8 %
Crystal growpH: 6.5
Details: 70-70% A.S. 210MM TRIS-HCL PH=6.5, 200MM SODIUM ACETATE
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-15 mg/mlprotein1drop
270-73 %satammonium sulfate1reservoir
3200 mMTris-HCl1reservoir
4200 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 15532 / % possible obs: 94.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 23.18 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.8 / % possible all: 91.9
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 19635 / Num. measured all: 52226
Reflection shell
*PLUS
% possible obs: 91.9 % / Rmerge(I) obs: 0.224

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Processing

Software
NameClassification
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.8 Å / SU B: 3.75 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.24 727 3 %RANDOM
Rwork0.183 ---
obs0.19 22500 100 %-
Displacement parametersBiso mean: 26.11 Å2
Refinement stepCycle: LAST / Resolution: 2→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 62 148 2420
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.2553
X-RAY DIFFRACTIONp_mcangle_it4.235
X-RAY DIFFRACTIONp_scbond_it7.2277
X-RAY DIFFRACTIONp_scangle_it10.03610
X-RAY DIFFRACTIONp_plane_restr0.024
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.2140.3
X-RAY DIFFRACTIONp_multtor_nbd0.2610.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor17.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor obs: 0.1797 / Rfactor Rfree: 0.2379
Solvent computation
*PLUS
Displacement parameters
*PLUS

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