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- PDB-3ntd: Structure of the Shewanella loihica PV-4 NADH-dependent persulfid... -

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Basic information

Entry
Database: PDB / ID: 3ntd
TitleStructure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C531S Mutant
ComponentsFAD-dependent pyridine nucleotide-disulphide oxidoreductase
KeywordsOXIDOREDUCTASE / FAD / CoA / persulfide reductase / rhodanese
Function / homology
Function and homology information


flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like 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 ...Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / FAD-dependent pyridine nucleotide-disulphide oxidoreductase
Similarity search - Component
Biological speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSazinsky, M.H. / Warner, M.D. / Lukose, V. / Lee, K.H. / Crane, E.J.
CitationJournal: Biochemistry / Year: 2010
Title: Characterization of an NADH-Dependent Persulfide Reductase from Shewanella loihica PV-4: Implications for the Mechanism of Sulfur Respiration via FAD-Dependent Enzymes .
Authors: Warner, M.D. / Lukose, V. / Lee, K.H. / Lopez, K. / H Sazinsky, M. / Crane, E.J.
History
DepositionJul 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: FAD-dependent pyridine nucleotide-disulphide oxidoreductase
B: FAD-dependent pyridine nucleotide-disulphide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,6568
Polymers122,4792
Non-polymers3,1776
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13630 Å2
ΔGint-63 kcal/mol
Surface area40860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.737, 133.737, 79.713
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 61239.520 Da / Num. of mol.: 2 / Mutation: C531S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: ATCC BAA-1088 / PV-4 / Gene: Shew_0729 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3QAV3, CoA-disulfide reductase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 50 mM Na acetate, 200 mM ammonium acetate, 5% PEG 8K, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2009
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.026
11K, H, -L20.323
11-h,-k,l30.651
ReflectionResolution: 1.99→116 Å / Num. all: 103268 / Num. obs: 103268 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rsym value: 0.092 / Net I/σ(I): 15.8
Reflection shellResolution: 1.99→2.07 Å / Mean I/σ(I) obs: 6.9 / Rsym value: 0.41 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ICR

3icr


Resolution: 1.99→115.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.411 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18465 5538 5.1 %RANDOM
Rwork0.15824 ---
obs0.15958 103268 99.32 %-
all-108806 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.884 Å2
Baniso -1Baniso -2Baniso -3
1--22.26 Å20 Å20 Å2
2---22.26 Å20 Å2
3---44.51 Å2
Refinement stepCycle: LAST / Resolution: 1.99→115.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8589 0 204 607 9400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0228923
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3531.99312117
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48651125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33124.433397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.636151480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5741562
X-RAY DIFFRACTIONr_chiral_restr0.1860.21368
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216708
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4341.55572
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.20228919
X-RAY DIFFRACTIONr_scbond_it3.90933351
X-RAY DIFFRACTIONr_scangle_it5.5314.53198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 386 -
Rwork0.213 7179 -
obs--93.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.89250.9802-0.53871.2129-0.37481.5993-0.012-0.0141-0.01520.0552-0.0202-0.124-0.04980.12190.03220.19270.00820.00280.1903-0.01310.202754.2813-10.733238.7706
20.8455-0.10910.5580.1652-0.0250.5813-0.03190.0080.09450.0013-0.00050.0003-0.0893-0.01380.03250.188-0.00390.01090.1611-0.00120.183844.2844-1.52524.133
31.59410.5186-0.35581.4233-0.32021.1973-0.00540.05170.0918-0.034-0.0113-0.1015-0.10190.10990.01660.22430.0081-0.01150.2445-0.00840.203932.4005-10.32162.3193
40.9919-0.63050.55580.7963-0.56480.65490.09640.1728-0.0184-0.1431-0.07820.03180.10380.1143-0.01830.2025-0.00990.01050.1937-0.0130.197551.829-9.988514.3563
50.73440.1899-0.24130.99810.14890.52220.02050.0054-0.03330.0280.0018-0.12360.00090.0855-0.02240.17550.0081-0.00220.16520.01170.150734.6796-30.237717.4037
61.14890.17790.31771.41560.16041.2464-0.00720.22650.0182-0.24690.00730.0236-0.0357-0.0349-0.00010.20570.00360.00440.21280.00380.20319.164-39.4619-5.945
70.3172-0.0429-0.07910.45360.26660.5129-0.002-0.009-0.0240.0134-0.00780.08410.0273-0.0750.00990.1661-0.0002-0.00550.18010.00540.17795.7283-51.897719.0332
81.369-0.5110.56240.89140.55791.56060.0014-0.10880.00270.0734-0.01070.0665-0.0015-0.10130.00930.1708-0.00920.01120.16240.01260.1693-0.4556-34.7239.1289
92.19430.2916-0.71580.9376-0.33590.939-0.0004-0.1012-0.08740.1038-0.00440.12760.0743-0.10990.00470.20540.0048-0.01310.1833-0.0130.16658.3122-32.979550.9583
100.2359-0.2756-0.0710.58140.1970.1032-0.0346-0.0758-0.0340.08260.0316-0.02910.05390.05870.0030.1972-0.0022-0.00250.20240.00550.189715.8328-52.8732.8111
110.9978-0.03110.03950.8231-0.13220.688-0.0060.0444-0.1004-0.01380.0104-0.01990.07850.0054-0.00440.0091-0.00020.00040.0198-0.00030.011930.2778-33.008633.9073
121.3670.23680.23031.26550.4361.26760.0073-0.22870.03960.2007-0.00380.0298-0.0352-0.0312-0.00360.18010.00460.0030.17190.0130.177639.561-20.373855.6884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 36
2X-RAY DIFFRACTION2A37 - 179
3X-RAY DIFFRACTION3A180 - 236
4X-RAY DIFFRACTION4A245 - 306
5X-RAY DIFFRACTION5A307 - 470
6X-RAY DIFFRACTION6A471 - 561
7X-RAY DIFFRACTION7B2 - 124
8X-RAY DIFFRACTION8B125 - 183
9X-RAY DIFFRACTION9B184 - 254
10X-RAY DIFFRACTION10B255 - 328
11X-RAY DIFFRACTION11B329 - 456
12X-RAY DIFFRACTION12B457 - 564

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