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- PDB-4jmt: Crystal structure of Cytochrome C Peroxidase W191G-Gateless in co... -

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Basic information

Entry
Database: PDB / ID: 4jmt
TitleCrystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 1H-pyrrolo[3,2-b]pyridin-6-ylmethanol
ComponentsCytochrome c peroxidase
KeywordsOXIDOREDUCTASE / Model system / bulk solvent / ordered waters / docking / ligand binding
Function / homology
Function and homology information


cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / cellular response to oxidative stress / mitochondrial matrix / heme binding / membrane / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1H-pyrrolo[3,2-b]pyridin-6-ylmethanol / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBarelier, S. / Fischer, M.
CitationJournal: To be published
Title: Docking to a water-filled model binding site in Cytochrome c Peroxidase
Authors: Barelier, S. / Boyce, S.E. / Fish, I. / Fischer, M. / Goodin, D.B. / Shoichet, B.K.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6933
Polymers32,9291
Non-polymers7652
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.470, 74.580, 51.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome c peroxidase /


Mass: 32928.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-362, DELETIONS G192-A193 / Mutation: P190G, W191G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: RM11-1a / Gene: CCP1 CCP CPO YKR066C, SCRG_04081 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3LRE1, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-1LZ / 1H-pyrrolo[3,2-b]pyridin-6-ylmethanol


Mass: 148.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Apo crystal grown in 100mM KPi, pH 6.0. Soaked into 100mM ZINC14401114 in 25% MPD (1h), vapor diffusion, sitting drop, temperature 283K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2011
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 54036 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHENIX1.6_289refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.186 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.17 / σ(F): 2 / Phase error: 15.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1752 2701 5 %
Rwork0.1576 --
obs0.1585 54001 98.77 %
all-56702 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.234 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 62.81 Å2 / Biso mean: 16.2123 Å2 / Biso min: 5.49 Å2
Baniso -1Baniso -2Baniso -3
1--5.4039 Å20 Å20 Å2
2--3.4695 Å2-0 Å2
3---1.9344 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 54 439 2821

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