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- PDB-4oxx: Crystal Structure of Cindoxin, Surface Entropy reduction Mutant -

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Basic information

Entry
Database: PDB / ID: 4oxx
TitleCrystal Structure of Cindoxin, Surface Entropy reduction Mutant
ComponentsCindoxin
KeywordsELECTRON TRANSPORT / Flavoprotein / FMN / Cindoxin
Function / homology
Function and homology information


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
FLAVIN MONONUCLEOTIDE / Cindoxin
Similarity search - Component
Biological speciesCitrobacter braakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.21 Å
AuthorsMadrona, Y. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM33688 United States
CitationJournal: Biochemistry / Year: 2014
Title: Crystal structure of cindoxin, the P450cin redox partner.
Authors: Madrona, Y. / Hollingsworth, S.A. / Tripathi, S. / Fields, J.B. / Rwigema, J.C. / Tobias, D.J. / Poulos, T.L.
History
DepositionFeb 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cindoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3282
Polymers16,8711
Non-polymers4561
Water4,107228
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-6 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.109, 82.109, 37.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

#1: Protein Cindoxin / Cdx / FMN-containing redox partner


Mass: 16871.490 Da / Num. of mol.: 1 / Mutation: E134A, E135A, E138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter braakii (bacteria) / Gene: cinC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q8VQF4
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 100mM hepes, pH 7, 1.7-2.1M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 43778 / % possible obs: 97 % / Redundancy: 3.5 % / Rsym value: 0.041 / Net I/σ(I): 31.8

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.7.3_928) / Classification: refinement
RefinementResolution: 1.21→32.852 Å / SU ML: 0.11 / σ(F): 1.36 / Phase error: 12.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1597 2213 5.06 %
Rwork0.141 --
obs0.1419 43762 98.95 %
Solvent computationShrinkage radii: 0.3 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.21→32.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 31 228 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141163
X-RAY DIFFRACTIONf_angle_d1.5761594
X-RAY DIFFRACTIONf_dihedral_angle_d14.03386
X-RAY DIFFRACTIONf_chiral_restr0.084188
X-RAY DIFFRACTIONf_plane_restr0.012205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.23450.2121530.17662554X-RAY DIFFRACTION98
1.2345-1.26320.19231230.1472596X-RAY DIFFRACTION100
1.2632-1.29480.1731450.12752577X-RAY DIFFRACTION100
1.2948-1.32980.17971250.11952608X-RAY DIFFRACTION100
1.3298-1.3690.13421530.10562654X-RAY DIFFRACTION100
1.369-1.41320.12691430.10852562X-RAY DIFFRACTION100
1.4132-1.46370.11151240.10342600X-RAY DIFFRACTION100
1.4637-1.52230.12811620.10352586X-RAY DIFFRACTION100
1.5223-1.59160.11551280.10292609X-RAY DIFFRACTION100
1.5916-1.67550.13381370.10522636X-RAY DIFFRACTION100
1.6755-1.78040.14961510.11972578X-RAY DIFFRACTION99
1.7804-1.91790.14661310.12532613X-RAY DIFFRACTION99
1.9179-2.11090.14591340.12772568X-RAY DIFFRACTION98
2.1109-2.41620.14671320.13832504X-RAY DIFFRACTION94
2.4162-3.04380.18391360.16712655X-RAY DIFFRACTION100
3.0438-32.8640.18561360.17052649X-RAY DIFFRACTION96

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