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- PDB-4jm9: Crystal structure of Cytochrome C Peroxidase W191G-Gateless in co... -

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Basic information

Entry
Database: PDB / ID: 4jm9
TitleCrystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 3-amino-1-methylpyridinium
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
PROTOPORPHYRIN IX CONTAINING FE / IODIDE ION / 1-METHYL-1,6-DIHYDROPYRIDIN-3-AMINE / 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.
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)33,8775
Polymers32,9291
Non-polymers9494
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.026, 74.702, 106.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 439 molecules

#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-LG5 / 1-METHYL-1,6-DIHYDROPYRIDIN-3-AMINE / 1-METHYL-1-LAMBDA-5-PYRIDIN-3-YL-AMINE


Mass: 110.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 60.12 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Apo crystal grown in 500mM MES, pH 6.0. Soaked into 50mM 3-amino-1-methylpyridinium, 25% MPD pH 4.5 (30min-1h), 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: Jun 16, 2009
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→61.2 Å / Num. obs: 79143

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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: 1.41→29.16 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.173 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1391 3976 5 %RANDOM
Rwork0.1149 ---
obs0.1161 79143 99.28 %-
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: 76.89 Å2 / Biso mean: 20.0436 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.41→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 57 435 2820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223081
X-RAY DIFFRACTIONr_bond_other_d0.0010.022120
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9974230
X-RAY DIFFRACTIONr_angle_other_deg0.99735186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69425.337163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40415533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.3291512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213666
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02651
X-RAY DIFFRACTIONr_mcbond_it1.7851.51802
X-RAY DIFFRACTIONr_mcbond_other0.6421.5729
X-RAY DIFFRACTIONr_mcangle_it2.5722937
X-RAY DIFFRACTIONr_scbond_it3.84231279
X-RAY DIFFRACTIONr_scangle_it5.1964.51286
X-RAY DIFFRACTIONr_rigid_bond_restr1.67535201
LS refinement shellResolution: 1.41→1.444 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 264 -
Rwork0.151 5192 -
all-5456 -
obs--94.02 %

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