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- PDB-2w5u: Flavodoxin from Helicobacter pylori in complex with the C3 inhibitor -

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Basic information

Entry
Database: PDB / ID: 2w5u
TitleFlavodoxin from Helicobacter pylori in complex with the C3 inhibitor
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / DRUG DISCOVERY / PROTEIN HINHIBITOR / FMN / TRANSPORT / FLAVODOXIN / FLAVOPROTEIN
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
FLAVIN MONONUCLEOTIDE / Chem-IC3 / Flavodoxin
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsCremades, N. / Perez-Dorado, I. / Hermoso, J.A. / Martinez-Julvez, M. / Sancho, J.
Citation
Journal: Acs Chem.Biol. / Year: 2009
Title: Discovery of Specific Flavodoxin Inhibitors as Potential Therapeutic Agents Against Helicobacter Pylori Infection.
Authors: Cremades, N. / Velazquez-Campoy, A. / Martinez-Julvez, M. / Neira, J.L. / Perez-Dorado, I. / Hermoso, J. / Jimenez, P. / Lanas, A. / Hoffman, P.S. / Sancho, J.
#1: 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.
#2: Journal: Biophys.Chem. / Year: 2005
Title: Towards a New Therapeutic Target: Helicobacter Pylori Flavodoxin.
Authors: Cremades, N. / Bueno, M. / Toja, M. / Sancho, J.
History
DepositionDec 12, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / struct_conn
Item: _entity.pdbx_description / _entity_src_gen.pdbx_host_org_vector_type
Revision 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 7, 2018Group: Database references / Category: citation / Item: _citation.year
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2925
Polymers35,0812
Non-polymers1,2113
Water1,60389
1
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2953
Polymers17,5401
Non-polymers7552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9972
Polymers17,5401
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.533, 50.967, 72.806
Angle α, β, γ (deg.)90.00, 98.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9559, -0.0105, -0.2936), (0.0095, -0.9999, 0.0046), (-0.2937, 0.0016, 0.9559)
Vector: 42.8578, 1.2355, -30.3947)

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Components

#1: Protein Flavodoxin


Mass: 17540.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET28A-FLDA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O25776
#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-IC3 / [2-(5-amino-4-cyano-1H-pyrazol-1-yl)-5-(trifluoromethyl)phenyl](hydroxy)oxoammonium


Mass: 298.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H7F3N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CONFLICTS LISTED IN THE SEQADV RECORDS BELOW ARE DUE TO THE FACT THAT THE PROTEIN ...THE SEQUENCE CONFLICTS LISTED IN THE SEQADV RECORDS BELOW ARE DUE TO THE FACT THAT THE PROTEIN SEQUENCE WAS OBTAINED DIRECTLY FROM THE H.PYLORI BACTERIA OF A PATIENT.

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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: 2.1 Å3/Da / Density % sol: 40.8 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: May 10, 2008 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.62→22 Å / Num. obs: 8523 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.7
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUE

1fue


Resolution: 2.62→22 Å / Cross valid method: THROUGHOUT
Details: AFTER MODEL REFINEMENT WITH CNS PROGRAM A LAST CYCLE OF REFINEMENT WAS PERFORMED USING REFMAC5 WITH TLS. INITIAL METEONINE RESIDUE WAS NOT OBSERVED NEITHER IN MOLECULE A NOR IN MOLECULE B
RfactorNum. reflection% reflectionSelection details
Rfree0.264 595 7 %RANDOM
Rwork0.227 ---
obs0.227 7928 99.8 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å2-0.55 Å2
2---0.34 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.62→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 83 89 2618
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.7721.5
X-RAY DIFFRACTIONc_mcangle_it1.432
X-RAY DIFFRACTIONc_scbond_it2.0533
X-RAY DIFFRACTIONc_scangle_it3.1174.5
LS refinement shellResolution: 2.62→2.69 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.283 / Total num. of bins used: 20

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