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- PDB-3nn3: Structure of chlorite dismutase from Candidatus Nitrospira defluv... -

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Basic information

Entry
Database: PDB / ID: 3nn3
TitleStructure of chlorite dismutase from Candidatus Nitrospira defluvii R173A 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: 2.6 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_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_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)141,96930
Polymers136,9665
Non-polymers5,00425
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-22 kcal/mol
Surface area50320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.740, 113.620, 120.520
Angle α, β, γ (deg.)90.00, 118.94, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
31A
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: 3 / Auth seq-ID: 1 - 238 / Label seq-ID: 4 - 241

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

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Components

#1: Protein
Chlorite dismutase


Mass: 27393.121 Da / Num. of mol.: 5 / Mutation: R173A
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.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.4M ammonium phosphate, 0.1M sodium acetate, pH 4.6, 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: Feb 26, 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: 2.6→105.4 Å / Num. obs: 50785 / % possible obs: 92.1 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.67 Å / % possible all: 79.9

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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: 2.6→44.39 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 23.361 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25434 2577 5.1 %RANDOM
Rwork0.212 ---
all0.2142 48167 --
obs0.2142 48167 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-4.3 Å2
2---1.83 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9565 0 315 175 10055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210125
X-RAY DIFFRACTIONr_bond_other_d0.0020.026790
X-RAY DIFFRACTIONr_angle_refined_deg1.2432.02313780
X-RAY DIFFRACTIONr_angle_other_deg0.881316430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61251185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.76323.404470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.864151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5661570
X-RAY DIFFRACTIONr_chiral_restr0.0670.21445
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022090
X-RAY DIFFRACTIONr_nbd_refined0.2090.22310
X-RAY DIFFRACTIONr_nbd_other0.1870.26627
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24677
X-RAY DIFFRACTIONr_nbtor_other0.0860.25180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.611.57663
X-RAY DIFFRACTIONr_mcbond_other0.1511.52420
X-RAY DIFFRACTIONr_mcangle_it0.72129480
X-RAY DIFFRACTIONr_scbond_it1.22135032
X-RAY DIFFRACTIONr_scangle_it1.7694.54290
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 positional0.040.05
2B1402tight positional0.030.05
3A1402tight positional0.020.05
4D1402tight positional0.030.05
5E1402tight positional0.030.05
1C1851loose positional0.85
2B1851loose positional0.755
3A1851loose positional0.755
4D1851loose positional0.75
5E1851loose positional0.655
1C1402tight thermal0.060.5
2B1402tight thermal0.060.5
3A1402tight thermal0.060.5
4D1402tight thermal0.060.5
5E1402tight thermal0.060.5
1C1851loose thermal0.7710
2B1851loose thermal0.8210
3A1851loose thermal0.6610
4D1851loose thermal0.7710
5E1851loose thermal0.6910
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 186 -
Rwork0.315 3587 -
obs--99.92 %
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)
12.5748-0.95830.39441.7898-0.18283.0768-0.3652-0.16080.53670.39040.0012-0.2812-0.93060.31230.36410.4596-0.1335-0.2529-0.132-0.01770.165914.68223.4327.49
22.14850.44980.00561.477-0.30774.10990.2262-0.0824-0.3840.2583-0.1544-0.25210.6910.4188-0.07180.37320.0263-0.1216-0.12160.120.045416.576-22.96326.837
31.2508-0.31010.81332.254-0.02524.173-0.00390.14470.14210.2962-0.0156-0.5737-0.02660.75950.0195-0.0393-0.096-0.10480.20760.1450.105131.5211.0522.714
42.0414-0.74460.85912.63510.4733.48920.1012-0.3783-0.20070.7835-0.21460.21420.4572-0.70190.11340.407-0.29480.04010.01780.0141-0.009-9.776-15.09734.527
51.6750.80811.04732.21840.61294.69110.0308-0.25680.20750.4768-0.24140.264-0.317-0.80290.21060.2530.1057-0.01030.0452-0.20960.0259-11.0213.42934.905
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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