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- PDB-2rbt: n-methylbenzylamine in complex with Cytochrome C Peroxidase W191G -

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Basic information

Entry
Database: PDB / ID: 2rbt
Titlen-methylbenzylamine in complex with Cytochrome C Peroxidase W191G
ComponentsCytochrome C Peroxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding ...cytochrome-c peroxidase / cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / 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 / membrane
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
N-methyl-1-phenylmethanamine / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Peroxidase / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.24 Å
AuthorsGraves, A.P. / Boyce, S.E. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
Authors: Graves, A.P. / Shivakumar, D.M. / Boyce, S.E. / Jacobson, M.P. / Case, D.A. / Shoichet, B.K.
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 30, 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
X: Cytochrome C Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2686
Polymers33,1991
Non-polymers1,0695
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.989, 75.752, 107.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Cytochrome C Peroxidase / E.C.1.11.1.5


Mass: 33198.867 Da / Num. of mol.: 1 / Mutation: W191G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: ccp1, ccp, cpo / Plasmid: PT7CCP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A7A026, UniProt: P00431*PLUS, cytochrome-c peroxidase

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Non-polymers , 5 types, 508 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-271 / N-methyl-1-phenylmethanamine


Mass: 121.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 291 K / pH: 6
Details: MES, MPD, pH 6.0, vapor diffusion, hanging drop, temperature 291K, pH 6.00

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2006
Details: VERTICAL FOCUSING MIRROR SINGLE CRYSTAL SI(311)BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
RadiationMonochromator: SIDE-SCATTERING CUBEROOT I- BEAM BENT SINGLE CRYSTAL; ASYMETRIC CUT 12.2 DEGS.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 109612 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.5
Reflection shellResolution: 1.24→1.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.407 / % possible all: 60.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
REFMACphasing
RefinementStarting model: 1AC4

1ac4


Resolution: 1.24→30 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.997 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.146 5452 5 %RANDOM
Rwork0.122 ---
obs0.123 109533 93.1 %-
all-109533 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.24→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 73 503 2920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222657
X-RAY DIFFRACTIONr_bond_other_d0.0020.021842
X-RAY DIFFRACTIONr_angle_refined_deg1.5942.0093647
X-RAY DIFFRACTIONr_angle_other_deg0.9773.0014469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02524.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03515444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9091513
X-RAY DIFFRACTIONr_chiral_restr0.1820.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023045
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02553
X-RAY DIFFRACTIONr_nbd_refined0.240.2589
X-RAY DIFFRACTIONr_nbd_other0.1950.22011
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21316
X-RAY DIFFRACTIONr_nbtor_other0.090.21272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0890.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5641.52010
X-RAY DIFFRACTIONr_mcbond_other0.7871.5621
X-RAY DIFFRACTIONr_mcangle_it1.9222488
X-RAY DIFFRACTIONr_scbond_it2.61131365
X-RAY DIFFRACTIONr_scangle_it3.2764.51133
X-RAY DIFFRACTIONr_rigid_bond_restr1.31235709
X-RAY DIFFRACTIONr_sphericity_free7.8623558
X-RAY DIFFRACTIONr_sphericity_bonded4.67834402
LS refinement shellResolution: 1.24→1.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 249 -
Rwork0.248 4744 -
obs--57.96 %

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