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- PDB-3nn2: Structure of chlorite dismutase from Candidatus Nitrospira defluv... -

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Basic information

Entry
Database: PDB / ID: 3nn2
TitleStructure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with cyanide
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / ferredoxin like fold / chlorite dismutation / periplasmatic
Function / homology
Function and homology information


chlorite O2-lyase / chlorite O2-lyase activity / heme binding / metal ion binding
Similarity search - Function
Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Chlorite dismutase
Similarity search - Component
Biological speciesCandidatus Nitrospira defluvii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKostan, J. / Sjoeblom, B. / Maixner, F. / Mlynek, G. / Furtmueller, P.G. / Obinger, C. / Wagner, M. / Daims, H. / Djinovic-Carugo, K.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue
Authors: Kostan, J. / Sjoeblom, B. / Maixner, F. / Mlynek, G. / Furtmueller, P.G. / Obinger, C. / Wagner, M. / Daims, H. / Djinovic-Carugo, K.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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_label_asym_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_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chlorite dismutase
B: Chlorite dismutase
C: Chlorite dismutase
D: Chlorite dismutase
E: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,51546
Polymers137,3965
Non-polymers6,11941
Water16,772931
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-25 kcal/mol
Surface area47750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.490, 145.490, 136.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Chlorite dismutase


Mass: 27479.236 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Nitrospira defluvii (bacteria)
Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3U4H7, chlorite O2-lyase

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Non-polymers , 5 types, 972 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CN
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / 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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M sodium/potassium phosphate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 26, 2008
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.94→125 Å / Num. all: 122022 / Num. obs: 121046 / % possible obs: 99.2 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.94→1.99 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE MODEL

Resolution: 1.94→32.836 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.585 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21152 6084 5 %RANDOM
Rwork0.1769 ---
all0.17866 114958 --
obs0.17866 114958 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.845 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0.39 Å20 Å2
2---0.78 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.94→32.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9620 0 393 931 10944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02110323
X-RAY DIFFRACTIONr_bond_other_d0.0010.026994
X-RAY DIFFRACTIONr_angle_refined_deg1.3222.02514009
X-RAY DIFFRACTIONr_angle_other_deg0.844316892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10551200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.16523.202481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69151729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7281576
X-RAY DIFFRACTIONr_chiral_restr0.0740.21454
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022154
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_it0.6471.55955
X-RAY DIFFRACTIONr_mcbond_other0.1741.52440
X-RAY DIFFRACTIONr_mcangle_it1.1929577
X-RAY DIFFRACTIONr_scbond_it1.7934368
X-RAY DIFFRACTIONr_scangle_it2.8564.54432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A972medium positional0.10.5
B972medium positional0.290.5
C972medium positional0.160.5
D972medium positional0.150.5
E972medium positional0.160.5
A1264loose positional0.515
B1264loose positional0.635
C1264loose positional0.575
D1264loose positional0.615
E1264loose positional0.595
A972medium thermal0.732
B972medium thermal0.842
C972medium thermal0.542
D972medium thermal0.512
E972medium thermal0.532
A1264loose thermal0.7410
B1264loose thermal0.710
C1264loose thermal0.6210
D1264loose thermal0.5810
E1264loose thermal0.5610
LS refinement shellResolution: 1.942→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 483 -
Rwork0.284 8445 -
obs--99.71 %
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)
11.7975-0.7095-1.13911.08240.84761.2668-0.070.1093-0.0325-0.1086-0.02690.105-0.035-0.16820.09690.05370.03640.01180.1354-0.00640.1543-13.31153.7712.722
21.7082-0.1467-0.55351.1993-0.010.9084-0.0055-0.27630.11590.2602-0.00150.07020.0308-0.01840.0070.0746-0.0570.040.2046-0.10550.112220.30153.4834.344
31.7754-0.373-0.37370.87530.50561.82250.1232-0.16550.4029-0.07420.0324-0.1013-0.2593-0.0625-0.15550.069-0.01070.07980.0586-0.06370.23877.62569.05314.146
41.87680.1376-0.60851.8971.06821.70820.0763-0.3596-0.06950.4357-0.10880.12880.36430.0120.03260.223-0.07990.13120.18720.00820.16366.68628.77135.251
51.2047-0.1444-0.6551.3728-0.73432.46060.11260.0489-0.06820.15120.15770.4016-0.063-0.3311-0.27020.1087-0.04330.15420.12020.0120.3834-13.61728.88315.696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 238
2X-RAY DIFFRACTION2B0 - 238
3X-RAY DIFFRACTION3C0 - 238
4X-RAY DIFFRACTION4D0 - 238
5X-RAY DIFFRACTION5E0 - 238

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