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- PDB-4jm5: Crystal structure of Cytochrome C Peroxidase W191G-Gateless in co... -

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Basic information

Entry
Database: PDB / ID: 4jm5
TitleCrystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 2-Amino-5-methylthiazole
ComponentsCytochrome c peroxidase
KeywordsOXIDOREDUCTASE / Model system / bulk solvent / ordered waters / docking / 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
2-AMINO-5-METHYLTHIAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsBoyce, S.E. / Fischer, M. / Fish, I. / Shoichet, B.K.
Citation
Journal: 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.
#1: Journal: To be Published
Title: Docking to a water-filled model binding site in Cytochrome c Peroxidase
Authors: Barelier, S. / Boyce, S.E. / Fischer, M. / Fish, I. / Goodin, D.B. / Shoichet, B.K.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _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)33,8554
Polymers32,9291
Non-polymers9273
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.314, 74.941, 106.643
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-25T / 2-AMINO-5-METHYLTHIAZOLE


Mass: 115.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7N2S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Co-crystal grown in 500mM MES, pH 6.0 and 25mM 2-amino-5-methylthiazole, 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 20, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.26→61.31 Å / Num. obs: 108085

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→30.26 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.097 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1547 5402 5 %RANDOM
Rwork0.1277 ---
obs0.129 108085 97.09 %-
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: 87.48 Å2 / Biso mean: 19.5701 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.26→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 62 508 2898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222688
X-RAY DIFFRACTIONr_angle_refined_deg1.8262.0073674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7895339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05125.248141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78515461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7091511
X-RAY DIFFRACTIONr_chiral_restr0.2490.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212163
X-RAY DIFFRACTIONr_mcbond_it2.1321.51563
X-RAY DIFFRACTIONr_mcangle_it2.9822528
X-RAY DIFFRACTIONr_scbond_it4.08731125
X-RAY DIFFRACTIONr_scangle_it5.5544.51134
X-RAY DIFFRACTIONr_rigid_bond_restr2.16232688
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 340 -
Rwork0.22 5993 -
all-6333 -
obs--78.79 %

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