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- PDB-1bu5: X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBORO... -

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Basic information

Entry
Database: PDB / ID: 1bu5
TitleX-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX
ComponentsPROTEIN (FLAVODOXIN)
KeywordsELECTRON TRANSPORT / FLAVOPROTEIN
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
RIBOFLAVIN / Flavodoxin
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWalsh, M.A. / Mccarthy, A. / O'Farrell, P.A. / Mccardle, P. / Cunningham, P.D. / Mayhew, S.G. / Higgins, T.M.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex.
Authors: Walsh, M.A. / McCarthy, A. / O'Farrell, P.A. / McArdle, P. / Cunningham, P.D. / Mayhew, S.G. / Higgins, T.M.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Comparison of the Crystal Structures of a Flavodoxin in its Three Oxidation States at Cryogenictemperatures
Authors: Watt, W. / Tulinsky, A. / Swenson, R.P. / Watenpaugh, K.D.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Cloning, Nucleotide Sequence, and Expression of the Flavodoxin Gene from Desulfovibrio Vulgaris (Hildenborough)
Authors: Krey, G.D. / Vanin, E.F. / Swenson, R.P.
#3: Journal: Fems Microbiol.Lett. / Year: 1988
Title: Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough
Authors: Curley, G.P. / Voordouw, G.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: The Binding of Riboflavin-5-Phosphate in a Flavoprotein. Flavodoxin at 2.0- Angstroms Resolution
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972
Title: Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstroms Resolution. Resolution of the Phase Ambiguity by Anomalous Scattering
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. / Legall, J. / Dubourdieu, M.
History
DepositionSep 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: 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 (FLAVODOXIN)
B: PROTEIN (FLAVODOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3536
Polymers31,4082
Non-polymers9454
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.380, 62.310, 77.420
Angle α, β, γ (deg.)90.00, 127.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.38919, -0.92107, 0.01285), (0.92109, -0.38896, 0.01745), (-0.01108, 0.01862, 0.99977)
Vector: 54.31591, -40.74148, -22.5735)

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Components

#1: Protein PROTEIN (FLAVODOXIN)


Mass: 15704.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00323
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growpH: 7
Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 ...Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 CONTAINING 1MM EDTA WITH A PROTEIN CONCENTRATION OF 10-15MG/ML. CRYSTALS APPEAR OVER 1-3 DAYS., pH 7.0
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160-80 %satammonium sulfate1drop
250 mMsodium phosphate1drop
31 mMEDTA1drop
410-15 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. obs: 26539 / % possible obs: 79.9 % / Observed criterion σ(I): -3 / Redundancy: 1.5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.3
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / % possible all: 83.2
Reflection
*PLUS
Num. measured all: 72050
Reflection shell
*PLUS
% possible obs: 83.2 %

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Processing

Software
NameClassification
AMoREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE FLAVODOXIN COORDINATES NOT DEPOSITED [M.A.WALSH PH.D THESIS NATIONAL UNIVERSITY OF IRELAND (1994)] BUT ESSENTIALLY IDENTICAL TO PDB ENTRY 2FX2

2fx2


Resolution: 1.83→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2037 0.08 %RANDOM
Rwork0.167 ---
obs0.169 26539 81 %-
Displacement parametersBiso mean: 27.1 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.83→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 64 197 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.184
X-RAY DIFFRACTIONp_mcangle_it4.45
X-RAY DIFFRACTIONp_scbond_it6.86
X-RAY DIFFRACTIONp_scangle_it10.38
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.230.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor20.1815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.4620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 0.08 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.150.17
X-RAY DIFFRACTIONp_mcbond_it43.18
X-RAY DIFFRACTIONp_scbond_it66.8
X-RAY DIFFRACTIONp_mcangle_it54.4
X-RAY DIFFRACTIONp_scangle_it810.3

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