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

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Basic information

Entry
Database: PDB / ID: 4nvk
TitlePredicting protein conformational response in prospective ligand discovery.
ComponentsCytochrome c peroxidase
KeywordsOXIDOREDUCTASE / Model system / flexibility / dynamic / loop / side-chains / energy penalty / occupancy / Boltzmann weights / flexible docking / ligand binding
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 / 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
N~2~,N~2~-diethylquinazoline-2,4-diamine / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 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
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: 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

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Assembly

Deposited unit
B: Cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8564
Polymers32,9291
Non-polymers9283
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.570, 71.610, 102.930
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
#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-2NY / N~2~,N~2~-diethylquinazoline-2,4-diamine


Mass: 216.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Compound soaked into crystal grown in equal volume of 500mM MES buffer (pH 6.0) and 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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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: Sep 18, 2012
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: 1.56→30.9 Å / Num. all: 53815 / Num. obs: 53815 / % possible obs: 99.8 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 2.1 / Redundancy: 4.3 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.7
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3925 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXdev_1391refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→30.9 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9007 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 16.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1737 2730 5.07 %RANDOM
Rwork0.1402 ---
obs0.1419 53814 99.73 %-
all-53814 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.79 Å2 / Biso mean: 23.0991 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: LAST / Resolution: 1.56→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 64 294 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192838
X-RAY DIFFRACTIONf_angle_d1.7713884
X-RAY DIFFRACTIONf_chiral_restr0.103361
X-RAY DIFFRACTIONf_plane_restr0.015531
X-RAY DIFFRACTIONf_dihedral_angle_d15.2391047
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.58870.26681410.206226812822100
1.5887-1.61920.21311550.172526052760100
1.6192-1.65230.2181450.152426662811100
1.6523-1.68820.21471350.146826562791100
1.6882-1.72750.19561280.139326592787100
1.7275-1.77070.1641220.129726712793100
1.7707-1.81850.16851450.129626862831100
1.8185-1.8720.18041470.135326632810100
1.872-1.93240.17241570.133126482805100
1.9324-2.00150.16291470.131326542801100
2.0015-2.08160.17461390.127326722811100
2.0816-2.17630.15111530.125326562809100
2.1763-2.2910.16341240.128327412865100
2.291-2.43450.18371490.131926632812100
2.4345-2.62240.18951540.132126792833100
2.6224-2.88610.16131440.139127172861100
2.8861-3.30340.17531450.14092713285899
3.3034-4.16030.14851520.129527632915100
4.1603-30.90.18181480.16542891303999

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