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- PDB-3nn1: Structure of chlorite dismutase from Candidatus Nitrospira defluv... -

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Basic information

Entry
Database: PDB / ID: 3nn1
TitleStructure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with imidazole
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
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / PHOSPHATE ION / Chlorite dismutase
Similarity search - Component
Biological speciesCandidatus Nitrospira defluvii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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_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.ptnr3_label_seq_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.ptnr1_label_seq_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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)142,80739
Polymers137,3965
Non-polymers5,41134
Water16,448913
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-22 kcal/mol
Surface area47870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.670, 145.670, 136.440
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
11D-46-

GLN

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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, 947 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.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 59.56 %
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: Nov 16, 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: 1.85→126 Å / Num. all: 276446 / Num. obs: 268021 / % possible obs: 97 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.9 Å / % possible all: 90.7

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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: 1.85→47.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.675 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20988 7117 5 %RANDOM
Rwork0.17998 ---
all0.18148 134596 --
obs0.18148 134596 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.19 Å20 Å2
2---0.39 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9595 0 351 913 10859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02110329
X-RAY DIFFRACTIONr_bond_other_d0.0020.027041
X-RAY DIFFRACTIONr_angle_refined_deg1.3992.02214030
X-RAY DIFFRACTIONr_angle_other_deg2.187316982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8951208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.04723.072485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.412151740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3271581
X-RAY DIFFRACTIONr_chiral_restr0.0790.21458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211344
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022202
X-RAY DIFFRACTIONr_mcbond_it0.7211.55975
X-RAY DIFFRACTIONr_mcbond_other0.1181.52446
X-RAY DIFFRACTIONr_mcangle_it1.25529619
X-RAY DIFFRACTIONr_scbond_it1.98634354
X-RAY DIFFRACTIONr_scangle_it3.0234.54411
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 535 -
Rwork0.216 9891 -
obs--100 %
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)
11.8365-0.7311-1.10790.97760.8031.1095-0.08190.0996-0.0355-0.0684-0.01520.1182-0.0046-0.16690.09710.03580.01820.00990.1212-0.01060.1274-13.18153.7522.617
21.3746-0.1707-0.53591.1630.0050.986-0.0221-0.25250.11570.23870.01820.11060.0262-0.03250.00390.0564-0.02560.04090.1464-0.08580.090720.37953.49634.339
31.4583-0.3591-0.47170.64810.42451.51610.1116-0.12070.3167-0.0640.022-0.0858-0.209-0.0631-0.13350.042-0.0020.06530.0223-0.04250.18947.67368.82514.083
41.63140.0605-0.5121.47860.84091.36030.0305-0.2667-0.07730.3938-0.07930.15990.3469-0.02520.04880.1996-0.04750.11640.08120.00760.13916.86928.82535.154
51.0076-0.2408-0.64081.3591-0.5652.32850.09290.0204-0.05330.16570.16550.4491-0.0739-0.3274-0.25840.0915-0.01890.15220.07370.00310.3324-13.55429.01815.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 238
2X-RAY DIFFRACTION2B1 - 238
3X-RAY DIFFRACTION3C1 - 238
4X-RAY DIFFRACTION4D1 - 238
5X-RAY DIFFRACTION5E1 - 238

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