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- PDB-4m09: Crystal Structure of Mutant Chlorite Dismutase from Candidatus Ni... -

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Basic information

Entry
Database: PDB / ID: 4m09
TitleCrystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W146Y R173Q
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 / SYNCHROTRON / Resolution: 2.45 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_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_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)141,77930
Polymers137,1365
Non-polymers4,64425
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25970 Å2
ΔGint-276 kcal/mol
Surface area47240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.100, 114.980, 118.870
Angle α, β, γ (deg.)90.000, 118.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-409-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid D
41chain E and segid F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid DC0
411chain E and segid FE0

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Chlorite dismutase


Mass: 27427.137 Da / Num. of mol.: 5 / Fragment: UNP residues 27-264 / Mutation: W146Y, R173Q
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, 190 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.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 3.5
Details: 0.8 M (NH4)2 SO4, 0.1 M citric acid pH 3.5, 1:1, hanging, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.2→44.38 Å / Num. obs: 72249 / % possible obs: 87.41 % / Redundancy: 3.2 % / Biso Wilson estimate: 26.13 Å2
Details: CC1/2 FOR WHOLE RANGE=0.99, CC1/2 FOR HIGH RESOLUTION SHELL=0.231
Rmerge(I) obs: 0.2338 / Net I/σ(I): 4.71
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 0.21 / Num. unique all: 3941 / % possible all: 47.9

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1388refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 2.45→44.38 Å / Occupancy max: 1 / Occupancy min: 0.61 / FOM work R set: 0.5996 / SU ML: 0.7 / σ(F): 0.95 / Phase error: 44.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3325 2976 5.03 %
Rwork0.2774 110020 -
obs0.2801 59180 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.61 Å2 / Biso mean: 68.1161 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: LAST / Resolution: 2.45→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9544 0 306 165 10015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310092
X-RAY DIFFRACTIONf_angle_d0.75113699
X-RAY DIFFRACTIONf_chiral_restr0.0251440
X-RAY DIFFRACTIONf_plane_restr0.0031725
X-RAY DIFFRACTIONf_dihedral_angle_d11.8863640
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4606X-RAY DIFFRACTION7.576TORSIONAL
12B4606X-RAY DIFFRACTION7.576TORSIONAL
13C4606X-RAY DIFFRACTION7.576TORSIONAL
14E4606X-RAY DIFFRACTION7.576TORSIONAL
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 (%)
2.45-2.47780.4481620.45543124328682
2.4778-2.5070.45511890.45663471366091
2.507-2.53760.41991920.43283554374698
2.5376-2.56970.46951980.43753739393798
2.5697-2.60350.44391860.43833608379498
2.6035-2.63910.42821960.42233766396298
2.6391-2.67680.40721940.42313613380798
2.6768-2.71680.48011960.41883724392098
2.7168-2.75920.43051910.40053648383998
2.7592-2.80450.46522010.39713739394098
2.8045-2.85280.46561920.40893636382898
2.8528-2.90470.42191800.37583781396199
2.9047-2.96050.38241920.35633640383299
2.9605-3.0210.42381630.35063782394599
3.021-3.08660.37152130.33173718393199
3.0866-3.15840.36592030.31353693389699
3.1584-3.23740.39941810.31193679386099
3.2374-3.32490.34831930.29643799399299
3.3249-3.42270.38161950.2853625382099
3.4227-3.53310.37681870.26933714390198
3.5331-3.65930.28542120.24263688390099
3.6593-3.80580.30192010.24593682388399
3.8058-3.97890.30342160.22493696391298
3.9789-4.18850.2722230.2033677390099
4.1885-4.45070.26222000.173701390199
4.4507-4.7940.23911830.1723744392799
4.794-5.27570.25681920.18473744393699
5.2757-6.03750.26622030.19473695389899
6.0375-7.60040.25771860.21893691387799
7.6004-44.39010.24742020.20033649385197
Refinement TLS params.Method: refined / Origin x: 8.7122 Å / Origin y: -0.7287 Å / Origin z: 28.8171 Å
111213212223313233
T0.1815 Å2-0.0952 Å2-0.0406 Å2-0.0882 Å20.0247 Å2--0.1027 Å2
L0.1149 °2-0.0178 °20.0172 °2-0.1472 °2-0.0133 °2--0.1322 °2
S-0.0563 Å °-0.0092 Å °0.0997 Å °0.1506 Å °-0.0586 Å °-0.088 Å °-0.1002 Å °0.0141 Å °-0.0628 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 239
2X-RAY DIFFRACTION1allB1 - 239
3X-RAY DIFFRACTION1allC3 - 239
4X-RAY DIFFRACTION1allD3 - 239
5X-RAY DIFFRACTION1allE2 - 239
6X-RAY DIFFRACTION1allK2 - 22
7X-RAY DIFFRACTION1allF1
8X-RAY DIFFRACTION1allS1 - 186

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