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- PDB-4oq7: Predicting protein conformational response in prospective ligand ... -

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Basic information

Entry
Database: PDB / ID: 4oq7
TitlePredicting protein conformational response in prospective ligand discovery.
ComponentsCytochrome c peroxidase
KeywordsOXIDOREDUCTASE / Model system / energy penalty / Boltzmann weights / flexible docking
Function / homology
Function and homology information


cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsFischer, M. / Fraser, J.S.
CitationJournal: Nat Chem / Year: 2014
Title: Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
Authors: Fischer, M. / Coleman, R.G. / Fraser, J.S. / Shoichet, B.K.
History
DepositionFeb 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Feb 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5452
Polymers32,9291
Non-polymers6161
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.350, 70.270, 102.800
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: UNP RESIDUES 72-362 / Mutation: 'P190G, W191G, DELETIONS G192-A193'
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: CRYSTAL GROWN IN EQUAL VOLUME OF 100MM KPI BUFFER (PH 6.0) AND 25% MPD, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2011
RadiationMonochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.89→38.025 Å / Num. all: 29781 / Num. obs: 29781 / % possible obs: 99.6 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 3.9 % / Biso Wilson estimate: 22.44 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.5
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2137 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
xia2data reduction
PHASERphasing
PHENIXdev_1565refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
XSCALEdata scaling
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→38.025 Å / FOM work R set: 0.8451 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1502 5.04 %RANDOM
Rwork0.175 ---
all0.175 29781 --
obs0.1771 29781 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.35 Å2 / Biso mean: 26.22 Å2 / Biso min: 12.28 Å2
Refinement stepCycle: LAST / Resolution: 1.89→38.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 43 194 2565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152550
X-RAY DIFFRACTIONf_angle_d1.3963478
X-RAY DIFFRACTIONf_chiral_restr0.089337
X-RAY DIFFRACTIONf_plane_restr0.008464
X-RAY DIFFRACTIONf_dihedral_angle_d14.963941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.9510.31471290.25822504263399
1.951-2.02070.25091480.22342499264799
2.0207-2.10170.25091300.203925512681100
2.1017-2.19730.24431320.194125462678100
2.1973-2.31310.2171210.184725432664100
2.3131-2.4580.25161340.180925472681100
2.458-2.64780.22381570.169125572714100
2.6478-2.91410.21331340.174325732707100
2.9141-3.33560.19781370.163625952732100
3.3356-4.20160.17631480.145326082756100
4.2016-38.03290.21481320.171427562888100

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