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- PDB-3qpi: Crystal Structure of Dimeric Chlorite Dismutases from Nitrobacter... -

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Basic information

Entry
Database: PDB / ID: 3qpi
TitleCrystal Structure of Dimeric Chlorite Dismutases from Nitrobacter winogradskyi
ComponentsChlorite Dismutase
KeywordsOXIDOREDUCTASE / Oxygen / Chlorite O(2)-lyase / cytoplasma / chlorite
Function / homology
Function and homology information


oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #3420 / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Uncharacterized protein
Similarity search - Component
Biological speciesNitrobacter winogradskyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMlynek, G. / Sjoeblom, B. / Kostan, J. / Fuereder, S. / Maixner, F. / Furtmueller, P.G. / Obinger, O. / Wagner, M. / Daims, H. / Djinovic-Carugo, K.
CitationJournal: J.Bacteriol. / Year: 2011
Title: Unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from Nitrobacter winogradskyi.
Authors: Mlynek, G. / Sjoblom, B. / Kostan, J. / Fureder, S. / Maixner, F. / Gysel, K. / Furtmuller, P.G. / Obinger, C. / Wagner, M. / Daims, H. / Djinovic-Carugo, K.
History
DepositionFeb 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Chlorite Dismutase
B: Chlorite Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7214
Polymers42,4882
Non-polymers1,2332
Water5,080282
1
A: Chlorite Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8612
Polymers21,2441
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chlorite Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8612
Polymers21,2441
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.620, 102.620, 49.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsAUTHORS HAVE CONFIRMED THE BIOLOGICAL UNIT BY PERFORMING SIZE EXCLUSION COLUMN

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Components

#1: Protein Chlorite Dismutase /


Mass: 21244.025 Da / Num. of mol.: 2 / Fragment: unp residues 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrobacter winogradskyi (bacteria) / Strain: Nb-255 / ATCC 25391 / Gene: Nwi_2442 / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: Q3SPU6, chlorite O2-lyase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 53.6 mM Na2HPO4, 846.4 mM NaH2PO4, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.278 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2009
RadiationMonochromator: channel cut ESRF monochromator Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 2.1→45.9 Å / Num. obs: 30125 / % possible obs: 79.9 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
DNAdata collection
AutoSolphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→45.893 Å / SU ML: 0.65 / σ(F): 6.84 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 1506 5 %
Rwork0.1933 --
obs0.1956 30125 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0129 Å20 Å20 Å2
2--0.0129 Å20 Å2
3---1.2794 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2730 0 86 282 3098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132900
X-RAY DIFFRACTIONf_angle_d1.3373968
X-RAY DIFFRACTIONf_dihedral_angle_d14.2471009
X-RAY DIFFRACTIONf_chiral_restr0.069417
X-RAY DIFFRACTIONf_plane_restr0.005495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.17520.37111490.35812830X-RAY DIFFRACTION99
2.1752-2.26230.3021490.27992831X-RAY DIFFRACTION100
2.2623-2.36530.25611480.23082841X-RAY DIFFRACTION100
2.3653-2.490.23851530.21332833X-RAY DIFFRACTION100
2.49-2.6460.26711470.1932858X-RAY DIFFRACTION100
2.646-2.85020.25611480.17862856X-RAY DIFFRACTION100
2.8502-3.1370.25411490.18732857X-RAY DIFFRACTION100
3.137-3.59080.23331490.16592861X-RAY DIFFRACTION100
3.5908-4.52340.17731580.14792890X-RAY DIFFRACTION100
4.5234-45.9040.22931560.18612962X-RAY DIFFRACTION100
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)
10.01750.0186-0.01750.02640.00690.21620.01110.02360.0136-0.0566-0.0092-0.02270.01610.0260.20190.12990.0086-0.01480.22490.08290.020311.786262.732412.3672
22.52160.1837-0.41780.7392-0.6341.6349-0.05060.2513-0.1478-0.18590.08660.16750.3001-0.18680.00930.2105-0.0310.04950.2301-0.00610.546411.679658.626310.411
30.5979-0.18790.61873.648-4.68526.26210.18170.14540.0852-0.16580.27480.29510.1894-0.2357-0.37250.16580.01760.03510.2088-0.0050.540810.979652.752915.5203
41.0739-0.11280.33481.2627-0.98610.8430.0531-0.0393-0.00990.1036-0.1728-0.2119-0.04340.05060.12360.1421-0.0171-0.00910.19130.00080.525921.707252.814427.5571
55.55021.636-0.53152.35481.04592.9796-0.0828-0.2729-0.14250.0257-0.1781-0.1219-0.08960.17480.17370.1922-0.0739-0.06990.25350.08970.571529.832556.126631.6354
61.09990.175-0.23921.3642-0.11521.0850.0664-0.0390.01790.1351-0.0504-0.1001-0.04480.1141-0.02130.1356-0.0124-0.00430.1750.00830.519518.621659.822122.338
71.54710.0990.40590.4222-0.12710.7479-0.08090.0472-0.07080.0271-0.1491-0.11890.05170.10090.15790.1516-0.00380.03880.22730.0340.608525.617358.431318.0104
82.4979-2.0047-0.07111.62680.375.48560.29240.0595-0.4223-0.011-0.07710.17780.4002-0.3737-0.17370.6223-0.0075-0.18990.33-0.07720.49642.857927.673513.2079
90.91630.0937-0.62441.94770.14411.132-0.01320.2489-0.2372-0.5262-0.00130.38720.2593-0.3054-0.03830.367-0.0472-0.09320.2728-0.11430.62730.562624.694319.6504
103.47732.47310.45451.77330.4551.3344-0.1172-0.07230.2631-0.3367-0.16250.19630.0745-0.10120.25360.2316-0.0093-0.02290.1764-0.04120.654113.654134.403222.5562
111.00730.1117-0.14780.4989-0.65140.85130.01710.1904-0.1683-0.3573-0.1565-0.09950.25520.02750.11730.24520.0479-0.04090.1564-0.07040.412915.93826.153125.8194
120.5043-0.4097-0.59642.0113-0.40053.7377-0.181-0.10880.05240.24710.1094-0.1252-0.30310.05270.0480.1851-0.0077-0.06290.2445-0.04210.405818.456237.674138.621
130.40180.1315-0.08381.24380.30551.0780.05790.0163-0.1861-0.3862-0.0389-0.03760.1450.0805-0.0050.2370.01520.00130.151-0.04830.491713.415226.127425.7113
141.1294-0.2339-0.07190.8504-0.09681.0073-0.0633-0.1385-0.09130.1487-0.0353-0.0130.1180.0468-0.1890.21090.0099-0.00190.18870.01370.0018.105623.949932.4724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:22)
2X-RAY DIFFRACTION2(chain A and resid 23:40)
3X-RAY DIFFRACTION3(chain A and resid 41:59)
4X-RAY DIFFRACTION4(chain A and resid 60:109)
5X-RAY DIFFRACTION5(chain A and resid 110:120)
6X-RAY DIFFRACTION6(chain A and resid 121:157)
7X-RAY DIFFRACTION7(chain A and resid 158:182)
8X-RAY DIFFRACTION8(chain B and resid 2:12)
9X-RAY DIFFRACTION9(chain B and resid 13:40)
10X-RAY DIFFRACTION10(chain B and resid 41:64)
11X-RAY DIFFRACTION11(chain B and resid 65:97)
12X-RAY DIFFRACTION12(chain B and resid 98:113)
13X-RAY DIFFRACTION13(chain B and resid 114:151)
14X-RAY DIFFRACTION14(chain B and resid 152:182)

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