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- PDB-4m05: Crystal Structure of Mutant Chlorite Dismutase from Candidatus Ni... -

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Basic information

Entry
Database: PDB / ID: 4m05
TitleCrystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii R173E
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Chlorite dismutase
Similarity search - Component
Biological speciesCandidatus Nitrospira defluvii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 / 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_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_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

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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)140,51813
Polymers137,2565
Non-polymers3,2638
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21960 Å2
ΔGint-141 kcal/mol
Surface area47700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.470, 112.390, 119.250
Angle α, β, γ (deg.)90.000, 117.840, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain E and segid E)
NCS domain segments: (Selection details: chain 'E' and segid 'E ')

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Components

#1: Protein
Chlorite dismutase


Mass: 27451.156 Da / Num. of mol.: 5 / Fragment: UNP residues 27-264 / Mutation: R173E
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
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: 40% (v/v) ethylene glycol, 0.1 M NaAc pH 4.5, 3:1, sitting, vapor diffusion, temperature 277K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2011
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.28→44.22 Å / Num. obs: 72249 / % possible obs: 99.6 % / Redundancy: 9.8 % / Biso Wilson estimate: 30.08 Å2
Details: CC1/2 FOR WHOLE RANGE=0.993, CC1/2 FOR HIGH RESOLUTION SHELL=0.129
Rmerge(I) obs: 0.371 / Net I/σ(I): 5.3
Reflection shellResolution: 2.28→2.361 Å / Redundancy: 5.8 % / Rmerge(I) obs: 6.865 / Mean I/σ(I) obs: 0.23 / Num. unique all: 6981

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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: 2.28→44.22 Å / Occupancy max: 1 / Occupancy min: 0.61 / FOM work R set: 0.6284 / SU ML: 0.6 / σ(F): 1.19 / Phase error: 41.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3201 7104 5.01 %random
Rwork0.268 ---
obs0.2706 72249 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.95 Å2 / Biso mean: 73.3882 Å2 / Biso min: 33.16 Å2
Refinement stepCycle: LAST / Resolution: 2.28→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9588 0 227 133 9948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910082
X-RAY DIFFRACTIONf_angle_d1.1613701
X-RAY DIFFRACTIONf_chiral_restr0.0451445
X-RAY DIFFRACTIONf_plane_restr0.0061732
X-RAY DIFFRACTIONf_dihedral_angle_d12.7573639
Refine LS restraints NCSNumber: 5801 / Type: POSITIONAL / Rms dev position: 7.878 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.30590.47672200.43094232445294
2.3059-2.3330.46082240.424364458895
2.333-2.36150.43712300.42264324455497
2.3615-2.39140.44212370.4254503474098
2.3914-2.42280.41422310.40784407463899
2.4228-2.4560.42672420.41634554479699
2.456-2.49110.39482320.408744634695100
2.4911-2.52830.40122430.387345544797100
2.5283-2.56780.37212330.380344484681100
2.5678-2.60990.38312440.380445894833100
2.6099-2.65490.41312390.39444804719100
2.6549-2.70320.40062380.376344744712100
2.7032-2.75510.39132410.374545794820100
2.7551-2.81140.35742370.351744904727100
2.8114-2.87250.41812220.365545144736100
2.8725-2.93930.44462550.336545254780100
2.9393-3.01280.34092820.313644594741100
3.0128-3.09420.33772280.304545264754100
3.0942-3.18530.38062210.299445464767100
3.1853-3.2880.33472270.309345564783100
3.288-3.40550.35482230.277245844807100
3.4055-3.54180.29662140.225945094723100
3.5418-3.70290.30272410.208845154756100
3.7029-3.8980.28262160.220445454761100
3.898-4.14210.25942330.197145364769100
4.1421-4.46160.24262410.160744984739100
4.4616-4.91010.242550.150545384793100
4.9101-5.61940.23832420.167744854727100
5.6194-7.07510.28072650.207945054770100
7.0751-44.22820.2262480.184145164764100
Refinement TLS params.Method: refined / Origin x: -8.6181 Å / Origin y: 0.0044 Å / Origin z: -28.8415 Å
111213212223313233
T0.8689 Å20.0137 Å2-0.2954 Å2-0.2897 Å20.0058 Å2--0.2187 Å2
L0.5419 °20.0509 °20.1955 °2-0.3681 °2-0.0674 °2--0.9426 °2
S-0.0755 Å °0.1394 Å °0.0957 Å °-0.196 Å °-0.0294 Å °0.0291 Å °0.0012 Å °-0.0141 Å °0.0291 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 238
2X-RAY DIFFRACTION1allB-1 - 238
3X-RAY DIFFRACTION1allC2 - 238
4X-RAY DIFFRACTION1allD1 - 238
5X-RAY DIFFRACTION1allE2 - 238
6X-RAY DIFFRACTION1allC1 - 301
7X-RAY DIFFRACTION1allA1 - 301
8X-RAY DIFFRACTION1allD1 - 301
9X-RAY DIFFRACTION1allB1 - 301
10X-RAY DIFFRACTION1allE1 - 301
11X-RAY DIFFRACTION1allC1 - 302
12X-RAY DIFFRACTION1allA - D1 - 425
13X-RAY DIFFRACTION1allD1 - 302
14X-RAY DIFFRACTION1allB1 - 302

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