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- PDB-2d5m: Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F) -

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Basic information

Entry
Database: PDB / ID: 2d5m
TitleFlavoredoxin of Desulfovibrio vulgaris (Miyazaki F)
Componentsflavoredoxin
KeywordsELECTRON TRANSPORT / flavoprotein / FMN binding
Function / homology
Function and homology information


FMN binding / metal ion binding
Similarity search - Function
Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / Flavoredoxin
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.05 Å
AuthorsUeda, Y. / Shibata, N. / Higuchi, Y.
CitationJournal: To be Published
Title: Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F)
Authors: Ueda, Y. / Shibata, N. / Higuchi, Y.
History
DepositionNov 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: flavoredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6936
Polymers20,8451
Non-polymers8485
Water4,666259
1
A: flavoredoxin
hetero molecules

A: flavoredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,38512
Polymers41,6902
Non-polymers1,69610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11370 Å2
ΔGint-237 kcal/mol
Surface area12790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.346, 53.346, 116.224
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-3217-

HOH

21A-3218-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: y-x, -x, z+2/3

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Components

#1: Protein flavoredoxin


Mass: 20844.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
Species: Desulfovibrio vulgaris / Strain: Miyazaki F / Plasmid: pMK2 / Production host: Escherichia coli (E. coli) / References: GenBank: 66766348, UniProt: Q4W5X6*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG8K, Zn acetate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 89930 / Num. obs: 89930 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.05→1.09 Å / % possible all: 97

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.05→10 Å / Num. parameters: 14389 / Num. restraintsaints: 17516 / Cross valid method: FREE R / σ(F): 0.9792 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1615 8966 -RANDOM
Rwork0.128 ---
all0.1352 80716 --
obs0.1352 80716 89.7 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 1401.18 / Occupancy sum non hydrogen: 1720.92
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 46 259 1722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.081
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0

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