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- PDB-4m06: Crystal Structure of Mutant Chlorite Dismutase from Candidatus Ni... -

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Basic information

Entry
Database: PDB / ID: 4m06
TitleCrystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145F in Complex with Cyanide
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Chlorite dismutase
Similarity search - Component
Biological speciesCandidatus Nitrospira defluvii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHagmueller, A. / Gysel, K. / 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 / 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_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)152,19318
Polymers148,7645
Non-polymers3,42913
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23390 Å2
ΔGint-128 kcal/mol
Surface area45270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.210, 113.420, 118.840
Angle α, β, γ (deg.)90.000, 117.940, 90.000
Int Tables number5
Space group name H-MC121
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: 29752.758 Da / Num. of mol.: 5 / Mutation: W145F
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, 18 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CN
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.53
Details: 0.78 M Ammonium citrate dibasic, 0.1 M Na acetate, 2:1, hanging, pH 4.53, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: Q315R CCD detector from ADSC / Detector: CCD / Date: Jul 19, 2012
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→43.45 Å / Num. obs: 47172 / % possible obs: 96 % / Redundancy: 7.2 % / Biso Wilson estimate: 59.84 Å2
Details: CC1/2 FOR WHOLE RANGE=0.998, CC1/2 FOR HIGH RESOLUTION SHELL=0.149
Rmerge(I) obs: 0.1423 / Net I/σ(I): 10.01
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 4.5 % / Rmerge(I) obs: 3.495 / Mean I/σ(I) obs: 0.38 / Num. unique all: 3833

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.45 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7074 / SU ML: 0.53 / σ(F): 0.95 / Phase error: 34.87 / Stereochemistry target values: ML / Details: CC1/2= 3.495
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 1921 4.08 %random
Rwork0.2111 ---
obs0.2131 47172 95.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.4 Å2 / Biso mean: 92.0237 Å2 / Biso min: 44.19 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9543 0 239 5 9787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510044
X-RAY DIFFRACTIONf_angle_d0.94413633
X-RAY DIFFRACTIONf_chiral_restr0.0511440
X-RAY DIFFRACTIONf_plane_restr0.0041721
X-RAY DIFFRACTIONf_dihedral_angle_d12.3193636
Refine LS restraints NCSNumber: 5793 / Type: POSITIONAL / Rms dev position: 6.54 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.63290.47361080.50362461256973
2.6329-2.66760.5461980.49352637273576
2.6676-2.70410.44441240.46172751287580
2.7041-2.74270.41821260.43562796292283
2.7427-2.78360.44751330.41722985311886
2.7836-2.82710.40371350.40933071320689
2.8271-2.87350.3951320.39163180331293
2.8735-2.9230.46361420.35723416355899
2.923-2.97620.39121460.330934423588100
2.9762-3.03340.41131470.302434063553100
3.0334-3.09530.33881410.275534083549100
3.0953-3.16260.35591490.2473489363899
3.1626-3.23610.26311430.230933633506100
3.2361-3.3170.28981460.238334363582100
3.317-3.40670.29871480.230934643612100
3.4067-3.50690.2361410.20373374351599
3.5069-3.620.26521380.192933753513100
3.62-3.74930.25861490.1934633612100
3.7493-3.89930.30761440.180334543598100
3.8993-4.07670.22661440.178434053549100
4.0767-4.29140.20931500.147734373587100
4.2914-4.560.20571440.136734563600100
4.56-4.91170.1881480.137334273575100
4.9117-5.40510.21711460.155534233569100
5.4051-6.18540.19661440.183134353579100
6.1854-7.78560.21671500.194734343584100
7.7856-43.46140.19491470.17373422356999
Refinement TLS params.Method: refined / Origin x: -8.55 Å / Origin y: -0.1964 Å / Origin z: -28.8153 Å
111213212223313233
T0.6245 Å20.0526 Å2-0.0937 Å2-0.5088 Å2-0.0166 Å2--0.4205 Å2
L1.074 °20.269 °20.1298 °2-1.1493 °2-0.2289 °2--1.1761 °2
S-0.0845 Å °0.1163 Å °0.1257 Å °-0.2421 Å °-0.06 Å °0.0513 Å °-0.0626 Å °-0.0293 Å °0.131 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 301
2X-RAY DIFFRACTION1allB0 - 301
3X-RAY DIFFRACTION1allC2 - 301
4X-RAY DIFFRACTION1allD4 - 301
5X-RAY DIFFRACTION1allE0 - 301
6X-RAY DIFFRACTION1allC1 - 302
7X-RAY DIFFRACTION1allA1 - 302
8X-RAY DIFFRACTION1allE1 - 302
9X-RAY DIFFRACTION1allA1 - 303
10X-RAY DIFFRACTION1allB1 - 302
11X-RAY DIFFRACTION1allD1 - 302
12X-RAY DIFFRACTION1allE1 - 303
13X-RAY DIFFRACTION1allC1 - 303
14X-RAY DIFFRACTION1allA - C1 - 403

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