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

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Basic information

Entry
Database: PDB / ID: 4jmz
TitleCrystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine
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
N-methyl-1H-benzimidazol-2-amine / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBarelier, S. / Fischer, M.
CitationJournal: Plos One / Year: 2013
Title: Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.
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 1.1Aug 28, 2013Group: 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 / 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)33,6923
Polymers32,9291
Non-polymers7642
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.150, 74.570, 51.180
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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-1M2 / N-methyl-1H-benzimidazol-2-amine


Mass: 147.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Apo crystal grown in 100mM KPi, pH 6.0. Soaked into 20mM ZINC00039393 (10min), vapor diffusion, sitting drop, temperature 283K

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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: 1.55→50 Å / Num. obs: 37823 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→28.97 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.914 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 1888 5.1 %RANDOM
Rwork0.1449 ---
obs0.1467 36760 99.79 %-
all-38648 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.38 Å2 / Biso mean: 20.911 Å2 / Biso min: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--1.01 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.82→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 54 482 2864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022553
X-RAY DIFFRACTIONr_bond_other_d0.0010.021731
X-RAY DIFFRACTIONr_angle_refined_deg2.3951.9743483
X-RAY DIFFRACTIONr_angle_other_deg0.93834208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92625.111135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82815419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9921511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212960
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02559
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 142 -
Rwork0.184 2323 -
all-2465 -
obs--100 %

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