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- PDB-3awh: E13K mutant of FMN-binding protein from Desulfovibrio vulgaris (M... -

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Basic information

Entry
Database: PDB / ID: 3awh
TitleE13K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
ComponentsFMN-binding protein
KeywordsFLAVOPROTEIN
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSato, S. / Nakanishi, T. / Inoue, H. / Kitamura, M.
CitationJournal: To be Published
Title: Crystal structure of E13K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Authors: Sato, S. / Nakanishi, T. / Inoue, H. / Kitamura, M.
History
DepositionMar 22, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FMN-binding protein
B: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2906
Polymers26,3062
Non-polymers9844
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-9 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.990, 60.865, 71.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FMN-binding protein


Mass: 13153.133 Da / Num. of mol.: 2 / Mutation: E13K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Miyazaki F / Gene: DvMF_2023 / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 5, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 31814 / % possible obs: 99.5 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.224

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLM

1flm


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.516 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20712 1605 5.1 %RANDOM
Rwork0.17747 ---
obs0.17896 30154 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.456 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2--2.6 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 64 283 2199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221952
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9912654
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3275242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.98322.56478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1515312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2081518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.51202
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12621926
X-RAY DIFFRACTIONr_scbond_it1.9033750
X-RAY DIFFRACTIONr_scangle_it3.1824.5728
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 135 -
Rwork0.258 2155 -
obs--100 %

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