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- PDB-2euu: Cytochrome c peroxidase (CCP) in complex with 1H-imidazol-2-ylmethanol -

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Basic information

Entry
Database: PDB / ID: 2euu
TitleCytochrome c peroxidase (CCP) in complex with 1H-imidazol-2-ylmethanol
Componentscytochrome c peroxidase
KeywordsOXIDOREDUCTASE / engineered ligand binding site
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1H-IMIDAZOL-2-YLMETHANOL / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBrenk, R. / Vetter, S.W. / Boyce, S.E. / Goodin, D.B. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Probing molecular docking in a charged model binding site.
Authors: Brenk, R. / Vetter, S.W. / Boyce, S.E. / Goodin, D.B. / Shoichet, B.K.
History
DepositionOct 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,1733
Polymers33,4581
Non-polymers7152
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.675, 73.521, 104.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cytochrome c peroxidase


Mass: 33458.258 Da / Num. of mol.: 1 / Mutation: W191G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pT7 CCP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, 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-BVG / 1H-IMIDAZOL-2-YLMETHANOL


Mass: 98.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM KPi 20% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 59787 / Num. obs: 59787 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.4
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.456 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1AEE

1aee


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.905 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16078 3005 5 %RANDOM
Rwork0.14528 ---
all0.14608 56600 --
obs0.14608 56600 98.42 %-
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 mean: 13.795 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2---0.72 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 50 339 2729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212461
X-RAY DIFFRACTIONr_bond_other_d0.0020.022079
X-RAY DIFFRACTIONr_angle_refined_deg1.32823343
X-RAY DIFFRACTIONr_angle_other_deg0.83234868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7485290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022775
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02505
X-RAY DIFFRACTIONr_nbd_refined0.2230.2528
X-RAY DIFFRACTIONr_nbd_other0.2410.22387
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9011.51444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48622313
X-RAY DIFFRACTIONr_scbond_it2.18131017
X-RAY DIFFRACTIONr_scangle_it3.254.51030
X-RAY DIFFRACTIONr_rigid_bond_restr1.16322461
X-RAY DIFFRACTIONr_sphericity_free3.2732339
X-RAY DIFFRACTIONr_sphericity_bonded1.70622390
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 195
Rwork0.208 3569

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