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- PDB-1flm: DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) -

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Basic information

Entry
Database: PDB / ID: 1flm
TitleDIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F)
ComponentsPROTEIN (FMN-BINDING PROTEIN)
KeywordsELECTRON TRANSPORT / FMN BINDING
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 / MIR / Resolution: 1.3 Å
AuthorsSuto, K. / Kawagoe, K. / Shibata, N. / Morimoto, K. / Higuchi, Y. / Kitamura, M. / Nakaya, T. / Yasuoka, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: How do the x-ray structure and the NMR structure of FMN-binding protein differ?
Authors: Suto, K. / Kawagoe, K. / Shibata, N. / Morimoto, Y. / Higuchi, Y. / Kitamura, M. / Nakaya, T. / Yasuoka, N.
History
DepositionMar 10, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 26, 2014Group: Other
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (FMN-BINDING PROTEIN)
B: PROTEIN (FMN-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2194
Polymers26,3062
Non-polymers9132
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-20 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.230, 84.600, 41.110
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99999, 0.00427, 0.00202), (-0.00335, -0.34022, -0.94034), (-0.00333, -0.94034, 0.34023)
Vector: 57.06046, 41.57248, 29.22138)

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Components

#1: Protein PROTEIN (FMN-BINDING PROTEIN)


Mass: 13153.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / Cellular location: CYTOPLASM / Plasmid: PMKBT-100 / Cellular location (production host): CYTOPLASM / 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.: 200 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 49.89 %
Crystal growpH: 7.5
Details: 20% PEG6000, 0.1M TRIS(PH7.5), 20% GRYCEROL, 0.2M NACL
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.1 MTris-HCl1drop
3200 mMsodium chloride1drop
40.1 MMES1reservoir
520 %(w/v)PEG60001reservoir
60.2 Msodium acetate1reservoir
70.2 Mglycerol1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Dec 15, 1997 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 68514 / % possible obs: 86.6 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 29
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 2 / % possible all: 60.6
Reflection
*PLUS
Num. measured all: 337547 / Rmerge(I) obs: 0.026
Reflection shell
*PLUS
% possible obs: 60.6 %

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Processing

Software
NameClassification
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 5694 -RANDOM
obs0.1503 51465 82.63 %-
all-51465 --
Refinement stepCycle: LAST / Resolution: 1.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 62 200 2114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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