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- PDB-4m07: Crystal Structure of Mutant Chlorite Dismutase from Candidatus Ni... -

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Basic information

Entry
Database: PDB / ID: 4m07
TitleCrystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145F
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Ferredoxin-like fold
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: 2.5 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 / 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

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)153,01926
Polymers148,7645
Non-polymers4,25621
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25810 Å2
ΔGint-103 kcal/mol
Surface area45760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.290, 112.610, 120.320
Angle α, β, γ (deg.)90.000, 118.490, 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

#1: Protein
Chlorite dismutase


Mass: 29752.758 Da / Num. of mol.: 5 / Fragment: UNP residues 27-264 / 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
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 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, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 315r / 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: 2.5→43.55 Å / Num. obs: 48975 / % possible obs: 87.29 % / Redundancy: 3 % / Biso Wilson estimate: 52.93 Å2
Details: CC1/2 FOR WHOLE RANGE=0.999, CC1/2 FOR HIGH RESOLUTION SHELL=0.148
Rmerge(I) obs: 0.06243 / Net I/σ(I): 12.64
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 1.9 % / Rmerge(I) obs: 3.033 / Mean I/σ(I) obs: 0.23 / Num. unique all: 2676

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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: 2.5→43.55 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6963 / SU ML: 0.52 / σ(F): 1.18 / Phase error: 35.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2535 1759 3.59 %Random
Rwork0.205 88457 --
obs0.2068 48932 83.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.4 Å2 / Biso mean: 94.3173 Å2 / Biso min: 38.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9524 0 291 47 9862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810064
X-RAY DIFFRACTIONf_angle_d1.10113639
X-RAY DIFFRACTIONf_chiral_restr0.0421438
X-RAY DIFFRACTIONf_plane_restr0.0061717
X-RAY DIFFRACTIONf_dihedral_angle_d13.8043645
Refine LS restraints NCSNumber: 5794 / Type: POSITIONAL / Rms dev position: 7.497 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.53570.4133570.45011669172638
2.5357-2.57350.4989840.45521877196143
2.5735-2.61380.4347940.4062110220447
2.6138-2.65660.448880.39822359244754
2.6566-2.70240.4255820.39772649273159
2.7024-2.75150.31251040.39872859296366
2.7515-2.80440.41711170.40133203332071
2.8044-2.86170.45481420.38453420356277
2.8617-2.92390.43141290.33863613374283
2.9239-2.99190.43041540.30794042419690
2.9919-3.06670.38191590.30384304446397
3.0667-3.14960.29281590.28464357451698
3.1496-3.24220.34591610.27184362452398
3.2422-3.34680.3681650.25864364452998
3.3468-3.46640.36191610.25124327448898
3.4664-3.60510.31771630.20034378454198
3.6051-3.76910.21721590.1774397455698
3.7691-3.96770.25151590.16314313447298
3.9677-4.21610.16531600.14114357451798
4.2161-4.54130.21361610.12054334449598
4.5413-4.99780.15961600.13034345450597
4.9978-5.71960.23091550.14944280443597
5.7196-7.20080.19071600.19184282444297
7.2008-43.55990.16391570.1594256441395
Refinement TLS params.Method: refined / Origin x: 8.3077 Å / Origin y: -0.2467 Å / Origin z: 29.0052 Å
111213212223313233
T0.6298 Å2-0.0515 Å2-0.1215 Å2-0.4143 Å20.0128 Å2--0.3242 Å2
L1.0437 °2-0.1241 °20.1987 °2-1.0872 °20.213 °2--1.2742 °2
S-0.0895 Å °-0.0838 Å °0.154 Å °0.2121 Å °-0.059 Å °-0.0375 Å °-0.0723 Å °0.0347 Å °0.1447 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 239
2X-RAY DIFFRACTION1allB0 - 239
3X-RAY DIFFRACTION1allC4 - 239
4X-RAY DIFFRACTION1allD4 - 239
5X-RAY DIFFRACTION1allE0 - 239
6X-RAY DIFFRACTION1allS3 - 75
7X-RAY DIFFRACTION1allF1
8X-RAY DIFFRACTION1allN1
9X-RAY DIFFRACTION1allP1
10X-RAY DIFFRACTION1allT1
11X-RAY DIFFRACTION1allK1
12X-RAY DIFFRACTION1allU1
13X-RAY DIFFRACTION1allQ1
14X-RAY DIFFRACTION1allV1
15X-RAY DIFFRACTION1allL1
16X-RAY DIFFRACTION1allR1
17X-RAY DIFFRACTION1allM1
18X-RAY DIFFRACTION1allW1
19X-RAY DIFFRACTION1allX1
20X-RAY DIFFRACTION1allY1
21X-RAY DIFFRACTION1allZ1
22X-RAY DIFFRACTION1alla1

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