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

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Basic information

Entry
Database: PDB / ID: 4nvn
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 / 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
2,3-dihydrobenzo[h][1,6]naphthyridin-4(1H)-one / 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: 1.47 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)34,0286
Polymers32,9291
Non-polymers1,1005
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.000, 73.440, 104.390
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-2O1 / 2,3-dihydrobenzo[h][1,6]naphthyridin-4(1H)-one


Mass: 198.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N2O
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
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: 1.47→31.5 Å / Num. all: 66685 / Num. obs: 66685 / % possible obs: 99.2 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 2.2 / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.4
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4587 / % possible all: 93.5

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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: 1.47→31.5 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9131 / SU ML: 0.14 / Isotropic thermal model: RANDOM / σ(F): 1.34 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1697 3376 5.06 %
Rwork0.1423 --
obs0.1437 66685 99.16 %
all-66685 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.51 Å2 / Biso mean: 19.1532 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: LAST / Resolution: 1.47→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 73 385 2786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192774
X-RAY DIFFRACTIONf_angle_d1.6283792
X-RAY DIFFRACTIONf_chiral_restr0.107354
X-RAY DIFFRACTIONf_plane_restr0.01512
X-RAY DIFFRACTIONf_dihedral_angle_d14.2561022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.49240.26611310.2212405253692
1.4924-1.51470.26581420.212520266296
1.5147-1.53830.24081420.19062567270998
1.5383-1.56360.21421320.165325972729100
1.5636-1.59050.17261340.138726522786100
1.5905-1.61940.17251380.127926252763100
1.6194-1.65060.16181570.125626172774100
1.6506-1.68430.16141380.124926232761100
1.6843-1.72090.16281360.120726412777100
1.7209-1.76090.17351280.123526542782100
1.7609-1.80490.17221250.12126432768100
1.8049-1.85370.16091380.131926232761100
1.8537-1.90830.16951540.13526442798100
1.9083-1.96990.19791440.131826502794100
1.9699-2.04030.13751490.126826272776100
2.0403-2.12190.16391410.130926532794100
2.1219-2.21850.17931450.130226422787100
2.2185-2.33540.161240.135926702794100
2.3354-2.48170.18791440.14126542798100
2.4817-2.67320.15381530.144626682821100
2.6732-2.9420.18371440.15082666281099
2.942-3.36730.16941390.144627032842100
3.3673-4.24080.12981560.134827312887100
4.2408-31.50.18421420.16312834297698

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