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- PDB-4m08: Crystal Structure of Mutant Chlorite Dismutase from Candidatus Ni... -

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Basic information

Entry
Database: PDB / ID: 4m08
TitleCrystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145V
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Ferredoxin-like fold
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 / Chlorite dismutase
Similarity search - Component
Biological speciesCandidatus Nitrospira defluvii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.799 Å
AuthorsGysel, K. / Hagmueller, A. / Djinovic-Carugo, K.
CitationJournal: Biochemistry / Year: 2014
Title: Manipulating conserved heme cavity residues of chlorite dismutase: effect on structure, redox chemistry, and reactivity.
Authors: Hofbauer, S. / Gysel, K. / Bellei, M. / Hagmuller, A. / Schaffner, I. / Mlynek, G. / Kostan, J. / Pirker, K.F. / Daims, H. / Furtmuller, P.G. / Battistuzzi, G. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / software / 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_auth_seq_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 / _software.name / _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

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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)143,12347
Polymers136,9615
Non-polymers6,16242
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.830, 145.830, 137.225
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain E) / NCS domain segments: (Selection details: chain 'E')

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Chlorite dismutase


Mass: 27392.158 Da / Num. of mol.: 5 / Fragment: UNP residues 27-264 / Mutation: W145V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Nitrospira defluvii (bacteria)
Gene: cld, cld1, NIDE1387 / Plasmid: pET21b Strep TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Tuner / References: UniProt: B3U4H7, chlorite O2-lyase

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Non-polymers , 5 types, 156 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#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.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4
Details: 1 M (NH4)2 SO4, 0.1 M citric acid pH 4.0, 2:1, hanging, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.799→63.15 Å / Num. obs: 41940 / % possible obs: 99.92 % / Redundancy: 35.5 % / Biso Wilson estimate: 49.69 Å2
Details: CC1/2 FOR WHOLE RANGE=0.998, CC1/2 FOR HIGH RESOLUTION SHELL=0.817
Rmerge(I) obs: 0.1957 / Net I/σ(I): 23.34
Reflection shellResolution: 2.799→2.899 Å / Redundancy: 21.9 % / Rmerge(I) obs: 1.657 / Mean I/σ(I) obs: 2.08 / Num. unique all: 4097 / % possible all: 99.39

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
PROTEUM PLUSPLUSdata collection
PROTEUM2data reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.799→63.146 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7533 / SU ML: 0.37 / σ(F): 1.33 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 1956 5.07 %
Rwork0.2205 36593 -
obs0.2236 38549 91.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.02 Å2 / Biso mean: 62.0942 Å2 / Biso min: 8.21 Å2
Refinement stepCycle: LAST / Resolution: 2.799→63.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9560 0 390 114 10064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410173
X-RAY DIFFRACTIONf_angle_d0.78313807
X-RAY DIFFRACTIONf_chiral_restr0.0311450
X-RAY DIFFRACTIONf_plane_restr0.0031730
X-RAY DIFFRACTIONf_dihedral_angle_d11.1633650
Refine LS restraints NCSNumber: 5818 / Type: POSITIONAL / Rms dev position: 5.381 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.799-2.86850.38571380.29632597273592
2.8685-2.94610.4061500.28042555270592
2.9461-3.03280.33571470.28252602274992
3.0328-3.13060.35991270.26012497262489
3.1306-3.24250.33851190.25582548266790
3.2425-3.37240.32491260.25472505263189
3.3724-3.52580.28131110.23822567267890
3.5258-3.71170.28771300.22012537266789
3.7117-3.94420.26771190.21622538265789
3.9442-4.24870.291550.19532539269490
4.2487-4.67610.24851550.18752603275892
4.6761-5.35250.22491580.18052684284294
5.3525-6.74230.2871660.23092837300398
6.7423-63.16230.23091550.20272984313999
Refinement TLS params.Method: refined / Origin x: -41.7509 Å / Origin y: 22.0739 Å / Origin z: 2.6719 Å
111213212223313233
T0.4942 Å2-0.1227 Å20.0704 Å2-0.447 Å20.1104 Å2--0.5139 Å2
L0.8173 °20.201 °20.1187 °2-1.3156 °2-0.1572 °2--0.7816 °2
S-0.1291 Å °0.1828 Å °0.0499 Å °-0.2191 Å °-0.007 Å °-0.4823 Å °-0.1586 Å °0.2858 Å °0.1058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 238
2X-RAY DIFFRACTION1allA301 - 430
3X-RAY DIFFRACTION1allB1 - 238
4X-RAY DIFFRACTION1allB301 - 427
5X-RAY DIFFRACTION1allC1 - 238
6X-RAY DIFFRACTION1allC301 - 450
7X-RAY DIFFRACTION1allD1 - 238
8X-RAY DIFFRACTION1allD301 - 412
9X-RAY DIFFRACTION1allE1 - 238
10X-RAY DIFFRACTION1allE301 - 412
11X-RAY DIFFRACTION1allF1 - 19
12X-RAY DIFFRACTION1allG1
13X-RAY DIFFRACTION1allH1
14X-RAY DIFFRACTION1allJ1

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