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- PDB-5gt2: Crystal Structure and Biochemical Features of dye-decolorizing pe... -

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Basic information

Entry
Database: PDB / ID: 5gt2
TitleCrystal Structure and Biochemical Features of dye-decolorizing peroxidase YfeX from Escherichia coli O157
ComponentsProbable deferrochelatase/peroxidase YfeX
KeywordsOXIDOREDUCTASE / YfeX / dye-decolorizing peroxidase / heme
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dye-decolorizing peroxidase YfeX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å
AuthorsMa, Y.L. / Yuan, Z.G. / Liu, S. / Wang, J.X. / Gu, L.C. / Liu, X.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp(143) and Arg(232) play divergent roles toward different substrates
Authors: Liu, X. / Yuan, Z. / Wang, J. / Cui, Y. / Liu, S. / Ma, Y. / Gu, L. / Xu, S.
History
DepositionAug 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Probable deferrochelatase/peroxidase YfeX
B: Probable deferrochelatase/peroxidase YfeX
C: Probable deferrochelatase/peroxidase YfeX
D: Probable deferrochelatase/peroxidase YfeX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,2608
Polymers136,7944
Non-polymers2,4664
Water13,745763
1
A: Probable deferrochelatase/peroxidase YfeX
C: Probable deferrochelatase/peroxidase YfeX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6304
Polymers68,3972
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-59 kcal/mol
Surface area23370 Å2
MethodPISA
2
B: Probable deferrochelatase/peroxidase YfeX
D: Probable deferrochelatase/peroxidase YfeX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6304
Polymers68,3972
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-59 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.574, 101.597, 114.300
Angle α, β, γ (deg.)90.00, 111.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-646-

HOH

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Components

#1: Protein
Probable deferrochelatase/peroxidase YfeX


Mass: 34198.438 Da / Num. of mol.: 4 / Mutation: V195M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yfeX, b2431, JW2424 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P76536, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 20% PEG3350 and 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 74489 / % possible obs: 98 % / Redundancy: 3.6 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2411: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.093→36.693 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.49
RfactorNum. reflection% reflection
Rfree0.2483 1995 2.68 %
Rwork0.2204 --
obs0.2211 74380 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.093→36.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9221 0 172 763 10156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059613
X-RAY DIFFRACTIONf_angle_d0.78113034
X-RAY DIFFRACTIONf_dihedral_angle_d17.6345605
X-RAY DIFFRACTIONf_chiral_restr0.0471356
X-RAY DIFFRACTIONf_plane_restr0.0041709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0932-2.14550.32481270.2694603X-RAY DIFFRACTION87
2.1455-2.20350.24931360.25124944X-RAY DIFFRACTION93
2.2035-2.26830.29261400.24995057X-RAY DIFFRACTION97
2.2683-2.34150.2371440.24795202X-RAY DIFFRACTION98
2.3415-2.42520.3131440.2565199X-RAY DIFFRACTION99
2.4252-2.52230.31181440.24785238X-RAY DIFFRACTION99
2.5223-2.63710.30271450.25285254X-RAY DIFFRACTION99
2.6371-2.7760.25961440.2475223X-RAY DIFFRACTION99
2.776-2.94990.2761440.23685258X-RAY DIFFRACTION99
2.9499-3.17750.24911450.23845256X-RAY DIFFRACTION99
3.1775-3.49710.25561450.21745270X-RAY DIFFRACTION100
3.4971-4.00260.23171460.20285284X-RAY DIFFRACTION99
4.0026-5.04080.20681440.17895285X-RAY DIFFRACTION99
5.0408-36.69860.19521470.18955312X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 18.7057 Å / Origin y: -22.1558 Å / Origin z: 26.1164 Å
111213212223313233
T0.0258 Å2-0.0215 Å2-0.039 Å2-0.0224 Å20.0163 Å2--0.093 Å2
L0.5793 °2-0.5824 °2-0.782 °2-0.9794 °21.1499 °2--1.8611 °2
S0.0309 Å °0.1085 Å °-0.0345 Å °-0.0236 Å °-0.1311 Å °0.0238 Å °0.0106 Å °-0.1877 Å °-0.1703 Å °
Refinement TLS groupSelection details: all

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