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- PDB-5de0: Dye-decolorizing protein from V. cholerae -

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Basic information

Entry
Database: PDB / ID: 5de0
TitleDye-decolorizing protein from V. cholerae
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / heme complex
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Deferrochelatase / TyrA protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsUchida, T. / Sasaki, M. / Tanaka, Y. / Yao, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT Japan
CitationJournal: Biochemistry / Year: 2015
Title: A Dye-Decolorizing Peroxidase from Vibrio cholerae.
Authors: Uchida, T. / Sasaki, M. / Tanaka, Y. / Ishimori, K.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deferrochelatase
B: Deferrochelatase
C: Deferrochelatase
D: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7838
Polymers135,3184
Non-polymers2,4664
Water4,540252
1
A: Deferrochelatase
B: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8924
Polymers67,6592
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-63 kcal/mol
Surface area24160 Å2
MethodPISA
2
C: Deferrochelatase
D: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8924
Polymers67,6592
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-63 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.700, 77.700, 156.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Deferrochelatase / Dyp-type peroxidase family protein


Mass: 33829.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: DN30_2082, VC39_07860, VC78_07860, VS27_03965, WG08_01515
Production host: Escherichia coli (E. coli) / References: UniProt: A0A085T8S6, UniProt: Q9KQ59*PLUS
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: potassium thiocyanate, PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 50860 / % possible obs: 99.8 % / Redundancy: 5.83 % / Rsym value: 0.12 / Net I/σ(I): 12.51
Reflection shellResolution: 2.24→2.38 Å / Redundancy: 5.72 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.4 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNR

3qnr


Resolution: 2.24→41.296 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 2542 5 %
Rwork0.2362 --
obs0.2368 50852 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→41.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9260 0 172 252 9684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039676
X-RAY DIFFRACTIONf_angle_d0.74513189
X-RAY DIFFRACTIONf_dihedral_angle_d13.5853465
X-RAY DIFFRACTIONf_chiral_restr0.0261442
X-RAY DIFFRACTIONf_plane_restr0.0031699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2404-2.28350.36461390.32612652X-RAY DIFFRACTION98
2.2835-2.33010.33341400.30922656X-RAY DIFFRACTION100
2.3301-2.38080.31541410.29432672X-RAY DIFFRACTION100
2.3808-2.43620.32791440.3012740X-RAY DIFFRACTION100
2.4362-2.49710.34851380.29372631X-RAY DIFFRACTION100
2.4971-2.56460.30491420.29542699X-RAY DIFFRACTION100
2.5646-2.640.33341420.28372681X-RAY DIFFRACTION100
2.64-2.72520.29971410.27562690X-RAY DIFFRACTION100
2.7252-2.82260.28171410.26892684X-RAY DIFFRACTION100
2.8226-2.93560.28461420.272688X-RAY DIFFRACTION100
2.9356-3.06920.27381420.26092706X-RAY DIFFRACTION100
3.0692-3.23090.30221420.26012698X-RAY DIFFRACTION100
3.2309-3.43330.28461410.24212678X-RAY DIFFRACTION100
3.4333-3.69820.23771430.22422712X-RAY DIFFRACTION100
3.6982-4.070.23241410.21482675X-RAY DIFFRACTION100
4.07-4.65830.17061400.18762662X-RAY DIFFRACTION100
4.6583-5.86630.18511430.19152709X-RAY DIFFRACTION100
5.8663-41.30270.1741400.17862677X-RAY DIFFRACTION100

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