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- PDB-3iwa: Crystal structure of a FAD-dependent pyridine nucleotide-disulphi... -

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Basic information

Entry
Database: PDB / ID: 3iwa
TitleCrystal structure of a FAD-dependent pyridine nucleotide-disulphide oxidoreductase from Desulfovibrio vulgaris
ComponentsFAD-dependent pyridine nucleotide-disulphide oxidoreductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


cell redox homeostasis / flavin adenine dinucleotide binding / oxidoreductase activity / metal ion binding
Similarity search - Function
: / Rhodanese Homology Domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase ...: / Rhodanese Homology Domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FAD-dependent pyridine nucleotide-disulfide oxidoreductase / FAD-dependent pyridine nucleotide-disulfide oxidoreductase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Iizuka, M. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a FAD-dependent pyridine nucleotide-disulphide oxidoreductase from Desulfovibrio vulgaris
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Iizuka, M. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: FAD-dependent pyridine nucleotide-disulphide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5942
Polymers50,5541
Non-polymers401
Water86548
1
A: FAD-dependent pyridine nucleotide-disulphide oxidoreductase
hetero molecules

A: FAD-dependent pyridine nucleotide-disulphide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1894
Polymers101,1092
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area3470 Å2
ΔGint-17 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.564, 127.564, 157.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Detailsprobable dimer

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Components

#1: Protein FAD-dependent pyridine nucleotide-disulphide oxidoreductase


Mass: 50554.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: DP4 / Gene: Dvul_0176 / Plasmid: modified pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A1V9T4, UniProt: A0A0H3A4H3*PLUS, Oxidoreductases; Acting on NADH or NADPH
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.5
Details: 100mM sodium cacodylate pH 5.5, 8% PEG 8K, 200mM calcium acetate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 18, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.3→32.09 Å / Num. all: 22125 / Num. obs: 22081 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3190 / Rsym value: 0.373 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.219 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.837 / SU B: 6.379 / SU ML: 0.157 / SU R Cruickshank DPI: 0.28 / SU Rfree: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.28 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1130 5.1 %RANDOM
Rwork0.208 ---
obs0.21 22046 99.82 %-
all-22086 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 86 Å2 / Biso mean: 47.86 Å2 / Biso min: 20.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20.91 Å20 Å2
2--1.82 Å20 Å2
3----2.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 1 48 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222965
X-RAY DIFFRACTIONr_bond_other_d0.0070.021924
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9654034
X-RAY DIFFRACTIONr_angle_other_deg0.9334726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72324.274117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75615486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6281522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_mcbond_it0.9181.51970
X-RAY DIFFRACTIONr_mcbond_other0.1511.5820
X-RAY DIFFRACTIONr_mcangle_it1.72323158
X-RAY DIFFRACTIONr_scbond_it2.3373995
X-RAY DIFFRACTIONr_scangle_it3.7784.5872
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 72 -
Rwork0.244 1521 -
all-1593 -
obs-1521 100 %

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