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- PDB-3nn4: Structure of chlorite dismutase from Candidatus Nitrospira defluv... -

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Basic information

Entry
Database: PDB / ID: 3nn4
TitleStructure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / ferredoxin like fold / chlorite dismutation / periplasmatic
Function / homologychlorite O2-lyase / chlorite O2-lyase activity / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / heme binding / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Chlorite dismutase
Function and homology information
Biological speciesCandidatus Nitrospira defluvii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)142,35631
Polymers137,2565
Non-polymers5,10026
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-26 kcal/mol
Surface area50380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.410, 113.880, 119.870
Angle α, β, γ (deg.)90.00, 118.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 2 / Auth seq-ID: 1 - 238 / Label seq-ID: 4 - 241

Dom-IDAuth asym-IDLabel asym-ID
1CC
2AA
3BB
4DD
5EE

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Components

#1: Protein
Chlorite dismutase


Mass: 27451.223 Da / Num. of mol.: 5 / Mutation: R173K
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
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 59.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.4-0.6M ammonium sulphate, 0.1M citric acid, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2009
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→106 Å / Num. obs: 44825 / % possible obs: 91.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.77 Å / % possible all: 80.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE MODEL

Resolution: 2.7→43.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 29.372 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25798 2256 5 %RANDOM
Rwork0.21609 ---
all0.21831 42510 --
obs0.21831 42510 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 77.041 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-8.42 Å2
2---2.13 Å20 Å2
3----5.48 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9585 0 320 195 10100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210149
X-RAY DIFFRACTIONr_bond_other_d0.0020.026830
X-RAY DIFFRACTIONr_angle_refined_deg1.3252.02513806
X-RAY DIFFRACTIONr_angle_other_deg0.909316530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56851185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34223.404470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.062151720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8011570
X-RAY DIFFRACTIONr_chiral_restr0.0710.21445
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211075
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022090
X-RAY DIFFRACTIONr_nbd_refined0.2110.22236
X-RAY DIFFRACTIONr_nbd_other0.1910.26689
X-RAY DIFFRACTIONr_nbtor_refined0.1850.24612
X-RAY DIFFRACTIONr_nbtor_other0.0860.25369
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2310
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1440.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.40.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4571.57675
X-RAY DIFFRACTIONr_mcbond_other0.211.52420
X-RAY DIFFRACTIONr_mcangle_it0.57429485
X-RAY DIFFRACTIONr_scbond_it1.16235042
X-RAY DIFFRACTIONr_scangle_it1.6944.54311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C1402tight positional0.050.05
2A1402tight positional0.030.05
3B1402tight positional0.040.05
4D1402tight positional0.030.05
5E1402tight positional0.040.05
1C1863medium positional0.570.5
2A1863medium positional0.520.5
3B1863medium positional0.50.5
4D1863medium positional0.520.5
5E1863medium positional0.560.5
1C1402tight thermal0.080.5
2A1402tight thermal0.060.5
3B1402tight thermal0.060.5
4D1402tight thermal0.060.5
5E1402tight thermal0.060.5
1C1863medium thermal0.412
2A1863medium thermal0.332
3B1863medium thermal0.392
4D1863medium thermal0.382
5E1863medium thermal0.372
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 163 -
Rwork0.315 3105 -
obs--99.82 %
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)
12.15850.99370.55272.20830.75033.3343-0.4110.07430.6119-0.30240.00420.2816-0.8736-0.18540.40680.07820.0878-0.11120.10110.02880.2368-14.97223.479-27.549
21.6946-0.66040.36611.3909-0.11384.80340.1851-0.0353-0.3427-0.2906-0.16230.23630.7274-0.4302-0.02280.0999-0.02690.05390.0629-0.13640.0534-16.694-23.049-27.042
31.02560.28781.11091.0588-0.56053.1868-0.0427-0.23460.17690.05350.01510.4025-0.0821-0.68930.0276-0.12450.05080.05480.3567-0.11540.1226-31.5420.972-22.823
41.37520.62241.05332.731-0.5523.38260.01650.1788-0.2567-0.7387-0.1903-0.35860.33920.60110.17370.140.22020.24730.21050.03990.03599.377-15.169-34.742
50.9825-0.53710.94232.4002-0.50923.6477-0.10720.15390.1695-0.4055-0.2208-0.2411-0.20020.79810.3280.0276-0.13260.11670.23820.24020.075810.52513.391-35.12
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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