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

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Basic information

Entry
Database: PDB / ID: 4nvi
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 / 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
3-bromoquinolin-4-amine / 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: 1.51 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 / 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
B: Cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1487
Polymers32,9291
Non-polymers1,2196
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.790, 73.500, 104.160
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-2NW / 3-bromoquinolin-4-amine


Mass: 223.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7BrN2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
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: Jul 11, 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: 1.51→31.4 Å / Num. all: 61321 / Num. obs: 61321 / % possible obs: 99.1 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 2.2 / Redundancy: 4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.9
Reflection shellResolution: 1.51→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4240 / % possible all: 97.7

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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: 1.51→31.4 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9078 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 15.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3103 5.06 %RANDOM
Rwork0.1452 ---
obs0.1469 61321 99.01 %-
all-61321 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.82 Å2 / Biso mean: 20.8295 Å2 / Biso min: 8.75 Å2
Refinement stepCycle: LAST / Resolution: 1.51→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 75 325 2728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172803
X-RAY DIFFRACTIONf_angle_d1.5423832
X-RAY DIFFRACTIONf_chiral_restr0.102358
X-RAY DIFFRACTIONf_plane_restr0.009518
X-RAY DIFFRACTIONf_dihedral_angle_d14.9641034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.53360.33111480.24392442259094
1.5336-1.55870.26421240.20482534265897
1.5587-1.58560.18541280.17032641276999
1.5856-1.61450.17871430.146226152758100
1.6145-1.64550.18081550.137926062761100
1.6455-1.67910.17561410.13626492790100
1.6791-1.71560.17541340.125626492783100
1.7156-1.75550.18691280.131526712799100
1.7555-1.79940.17061230.128526582781100
1.7994-1.8480.17291400.134726182758100
1.848-1.90240.17051540.142626732827100
1.9024-1.96380.20581470.140126382785100
1.9638-2.0340.15371520.131226342786100
2.034-2.11540.16841390.13462648278799
2.1154-2.21170.1891470.13192634278199
2.2117-2.32820.17131210.13362677279899
2.3282-2.4740.16691440.13882631277599
2.474-2.6650.14671530.142653280699
2.665-2.9330.17271450.15432668281399
2.933-3.3570.18771430.14652699284299
3.357-4.22780.15591510.139627382889100
4.2278-31.40.20351430.16472842298598

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