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- PDB-2e83: T31V mutant of FMN-binding protein from Desulfovibrio vulgaris (M... -

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Basic information

Entry
Database: PDB / ID: 2.0E+83
TitleT31V mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
ComponentsFMN-binding protein
KeywordsELECTRON TRANSPORT / BETA SHEET
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-binding protein
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsShibata, N. / Higuchi, Y.
CitationJournal: To be Published
Title: Structure of T31V mutant of FMN-binding protein from Desulfovibrio vulgaris Miyazaki F
Authors: Shibata, N. / Kitamura, M. / Higuchi, Y.
History
DepositionJan 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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 1.3Oct 25, 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: FMN-binding protein
B: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2154
Polymers26,3022
Non-polymers9132
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.615, 84.394, 40.387
Angle α, β, γ (deg.)90.00, 93.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FMN-binding protein


Mass: 13151.094 Da / Num. of mol.: 2 / Mutation: T31V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
Species: Desulfovibrio vulgaris / Strain: Miyazaki F / Plasmid: pMKBT-100 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q46604
#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.: 393 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG 6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. all: 37400 / Num. obs: 37400 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 25.26
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 8.29 / Num. unique all: 3491 / % possible all: 92.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLM

1flm


Resolution: 1.52→26.33 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 699172.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3716 10 %RANDOM
Rwork0.161 ---
obs0.161 37117 98.5 %-
all-37373 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8092 Å2 / ksol: 0.366753 e/Å3
Displacement parametersBiso mean: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20.3 Å2
2---0.4 Å20 Å2
3---0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.01 Å
Refinement stepCycle: LAST / Resolution: 1.52→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 62 393 2307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.52→1.57 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.21 369 10.7 %
Rwork0.179 3082 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fmn.paramfmn.top

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