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- PDB-2bmv: Apoflavodoxin from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2bmv
TitleApoflavodoxin from Helicobacter pylori
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / FLAVOPROTEIN / HELICOBACTER PYLORI / FMN / TRANSPORT PROTEIN
Function / homology
Function and homology information


Flavodoxin, long chain / : / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / Flavodoxin
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMartinez-Julvez, M. / Hermoso, J.A. / Sancho, J. / Perez-Dorado, I. / Cremades, N. / Bueno, M.
Citation
Journal: Proteins / Year: 2007
Title: Common Conformational Changes in Flavodoxins Induced by Fmn and Anion Binding: The Structure of Helicobacter Pylori Apoflavodoxin.
Authors: Martinez-Julvez, M. / Cremades, N. / Bueno, M. / Perez-Dorado, I. / Maya, C. / Cuesta-Lopez, S. / Prada, D. / Falo, F. / Hermoso, J.A. / Sancho, J.
#1: Journal: Biophys.Chem. / Year: 2005
Title: Towards a Nwe Therapeutic Target: Helicobacter Pylori Flavodoxin
Authors: Cremades, N. / Buen, M. / Toja, M. / Sancho, J.
History
DepositionMar 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6683
Polymers17,5121
Non-polymers1562
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.610, 45.712, 86.652
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 FLAVODOXIN


Mass: 17512.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria)
Description: THE GENE THAT WAS EXPRESSED TO OBTAIN THE PROTEIN WAS ISOLATED FROM A PATIENT INFECTED WITH H.PYLORI SP.
Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O25776
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS REPORT THAT DISCREPANCIES IN SEQUENCE ARE DUE TO THE FACT THAT THE GENE WAS ISOLATED ...THE AUTHORS REPORT THAT DISCREPANCIES IN SEQUENCE ARE DUE TO THE FACT THAT THE GENE WAS ISOLATED FROM A PATIENT INFECTED WITH H.PYLORI. THE CONFLICTS REPORTED BELOW COULD BE THAT FROM A VARIANT STRAIN OF THE BACTERIA.

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ROTATING ANODE / Wavelength: 1.5418
DetectorType: BRUCKER-NONIUS / Detector: CCD / Date: Oct 25, 2004 / Details: MONTEL MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→20.3 Å / Num. obs: 9402 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 11.8
Reflection shellResolution: 2.11→2.18 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.56 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUE

1fue


Resolution: 2.11→9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.875 / SU B: 7.122 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 625 7.2 %RANDOM
Rwork0.2 ---
obs0.206 8016 100 %-
Displacement parametersBiso mean: 19.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.11→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 10 111 1349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211256
X-RAY DIFFRACTIONr_bond_other_d0.0020.021095
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9421693
X-RAY DIFFRACTIONr_angle_other_deg0.82932561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021440
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02252
X-RAY DIFFRACTIONr_nbd_refined0.2180.2284
X-RAY DIFFRACTIONr_nbd_other0.2490.21244
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.2716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6391.5799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17721266
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9773457
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0774.5427
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 43
Rwork0.259 520
Refinement TLS params.Method: refined / Origin x: 6.099 Å / Origin y: 21.977 Å / Origin z: 33.493 Å
111213212223313233
T0.0093 Å2-0.0258 Å2-0.0018 Å2-0.0728 Å20.0093 Å2--0.043 Å2
L2.4179 °20.5031 °2-0.628 °2-1.5998 °20.0464 °2--1.1346 °2
S-0.1249 Å °0.2349 Å °0.0867 Å °0.0365 Å °0.1649 Å °-0.0731 Å °0.0396 Å °-0.0909 Å °-0.04 Å °

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