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- PDB-5nkv: Crystal structure of dimeric chlorite dismutase from Cyanothece s... -

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Basic information

Entry
Database: PDB / ID: 5nkv
TitleCrystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 at pH 9.0 and 293 K.
ComponentsChlorite Dismutase
KeywordsOXIDOREDUCTASE / chlorite dismutase / cyanobacteria / heme / ferredoxin-like fold
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #3420 / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / hydrogen peroxide-dependent heme synthase
Similarity search - Component
Biological speciesCyanothece sp. PCC 7425 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPuehringer, D. / Schaffner, I. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
CitationJournal: ACS Catal / Year: 2017
Title: Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies.
Authors: Schaffner, I. / Mlynek, G. / Flego, N. / Puhringer, D. / Libiseller-Egger, J. / Coates, L. / Hofbauer, S. / Bellei, M. / Furtmuller, P.G. / Battistuzzi, G. / Smulevich, G. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionApr 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlorite Dismutase
B: Chlorite Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,48311
Polymers43,6622
Non-polymers1,8219
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-60 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.427, 53.015, 55.337
Angle α, β, γ (deg.)107.300, 98.540, 109.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Chlorite Dismutase


Mass: 21830.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. PCC 7425 (bacteria) / Gene: Cyan7425_1434 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B8HNS6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.5
Details: 0.15 M MgSO4, 0.1 M MES pH 6.5, 30% PEG 3350 grown in capillary counter-diffusion set up and buffer exchanged for 0.15 M MgSO4, 0.1 M Tris HCl pH 9.0, 30% PEG 3350, all dissolved in D2O.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→19.489 Å / Num. obs: 27988 / % possible obs: 80.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 25.74 Å2 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1457 / % possible all: 42.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2689refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.489 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.33
RfactorNum. reflection% reflection
Rfree0.186 1307 4.67 %
Rwork0.1595 --
obs0.1607 27983 80.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.62 Å2 / Biso mean: 48.4025 Å2 / Biso min: 9.35 Å2
Refinement stepCycle: final / Resolution: 2→19.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 231 138 3316
Biso mean--53.51 38.75 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033147
X-RAY DIFFRACTIONf_angle_d0.5814274
X-RAY DIFFRACTIONf_chiral_restr0.041432
X-RAY DIFFRACTIONf_plane_restr0.002537
X-RAY DIFFRACTIONf_dihedral_angle_d13.5331824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.080.2072750.18381571164643
2.08-2.17460.2581900.19432086217657
2.1746-2.2890.21621460.18722514266069
2.289-2.43220.24961630.18923009317283
2.4322-2.61960.21431560.1813470362694
2.6196-2.88240.19611690.18083466363594
2.8824-3.29780.20081490.18123485363495
3.2978-4.14830.1721750.13683503367895
4.1483-19.48950.14921840.13433572375697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.28710.90713.25172.14820.95087.69520.07820.9474-0.1866-0.23870.08210.01860.43870.9650.01380.14320.0630.02390.2335-0.04660.186-6.6308-1.263-0.4554
23.06750.4372.90322.2131.15497.8924-0.1643-0.56430.3040.2761-0.25280.1062-0.5012-0.77460.01730.13380.03270.00570.1411-0.0510.1672-6.52978.324429.7206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 182)A1 - 182
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 182)B1 - 182

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