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

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Basic information

Entry
Database: PDB / ID: 4jpu
TitleCrystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with Benzamidine
ComponentsCytochrome c peroxidase
KeywordsOXIDOREDUCTASE / Model system / ligand binding / free energy calculation / molecular dynamics
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
BENZAMIDINE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBoyce, S.E. / Fischer, M. / Fish, I.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Blind prediction of charged ligand binding affinities in a model binding site.
Authors: Rocklin, G.J. / Boyce, S.E. / Fischer, M. / Fish, I. / Mobley, D.L. / Shoichet, B.K. / Dill, K.A.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Feb 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)33,8555
Polymers32,9291
Non-polymers9274
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.851, 74.809, 106.753
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-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Apo crystal grown in 500mM MES, pH 6.0. Soaked into 50mM Benzamidine, 25% MPD pH 4.5 (30min-1hr), 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.41→61.31 Å / Num. obs: 78538

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→29.16 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0.715 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1617 3942 5 %RANDOM
Rwork0.1436 ---
obs0.1445 78538 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 55.11 Å2 / Biso mean: 21.377 Å2 / Biso min: 12.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.41→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 62 437 2827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222796
X-RAY DIFFRACTIONr_bond_other_d0.0010.021894
X-RAY DIFFRACTIONr_angle_refined_deg1.8272.0013833
X-RAY DIFFRACTIONr_angle_other_deg0.99834611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0485348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73525.166151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94315463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.6231512
X-RAY DIFFRACTIONr_chiral_restr0.1210.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02599
X-RAY DIFFRACTIONr_mcbond_it1.0191.51628
X-RAY DIFFRACTIONr_mcbond_other0.3111.5658
X-RAY DIFFRACTIONr_mcangle_it1.72622645
X-RAY DIFFRACTIONr_scbond_it2.48931168
X-RAY DIFFRACTIONr_scangle_it3.864.51188
LS refinement shellResolution: 1.41→1.448 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 246 -
Rwork0.243 5260 -
all-5506 -
obs--96.01 %

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