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- PDB-5u61: CcP gateless cavity -

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Basic information

Entry
Database: PDB / ID: 5u61
TitleCcP gateless cavity
ComponentsPeroxidase
KeywordsOXIDOREDUCTASE / Model system / Cytochrome c Peroxidase / GIST / desolvation / 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
5-cyclopropyl-1H-imidazol-2-amine / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.222 Å
AuthorsFischer, M. / Shoichet, B.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM59957 OD009180 GM110580 United States
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Testing inhomogeneous solvation theory in structure-based ligand discovery.
Authors: Balius, T.E. / Fischer, M. / Stein, R.M. / Adler, T.B. / Nguyen, C.N. / Cruz, A. / Gilson, M.K. / Kurtzman, T. / Shoichet, B.K.
#1: Journal: 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 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6683
Polymers32,9291
Non-polymers7402
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.032, 74.782, 106.831
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 Peroxidase


Mass: 32928.582 Da / Num. of mol.: 1 / Mutation: P190G, W191G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast)
Strain: RM11-1a / Gene: SCRG_04081 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B3LRE1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Mutation: P190G, W191G / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-7WG / 5-cyclopropyl-1H-imidazol-2-amine


Mass: 123.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.04 Å3/Da / Density % sol: 59.54 % / Mosaicity: 0 °
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 13, 2016
RadiationMonochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.22→106.83 Å / Num. obs: 87558 / % possible obs: 72.1 % / Redundancy: 12.4 % / Biso Wilson estimate: 11.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.011 / Rrim(I) all: 0.041 / Net I/σ(I): 29.5 / Num. measured all: 1084844 / Scaling rejects: 1198
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.22-1.265.50.1960.978111
5.33-106.8311.70.0250.999198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.67 Å53.42 Å
Translation6.67 Å53.42 Å

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHASER2.6.1phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.222→53.416 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.64
RfactorNum. reflection% reflection
Rfree0.1408 4370 5 %
Rwork0.1204 --
obs0.1214 87459 72.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.06 Å2 / Biso mean: 16.7351 Å2 / Biso min: 6.82 Å2
Refinement stepCycle: final / Resolution: 1.222→53.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 19 340 2730
Biso mean--19.15 25.73 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082612
X-RAY DIFFRACTIONf_angle_d1.3243563
X-RAY DIFFRACTIONf_chiral_restr0.072344
X-RAY DIFFRACTIONf_plane_restr0.006478
X-RAY DIFFRACTIONf_dihedral_angle_d13.831959
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2221-1.2360.2564170.1872843018
1.236-1.25060.2006230.157748050313
1.2506-1.26580.1451390.139660164016
1.2658-1.28190.2075490.130875180020
1.2819-1.29870.1751470.133692897525
1.2987-1.31650.1615500.12361088113828
1.3165-1.33530.1469600.12531269132933
1.3353-1.35530.1629800.12311498157840
1.3553-1.37640.1371910.11231752184346
1.3764-1.3990.1441060.11552047215354
1.399-1.42310.14251160.11142430254663
1.4231-1.4490.12031480.10642971311978
1.449-1.47690.13581850.10563558374393
1.4769-1.5070.13691810.10833599378094
1.507-1.53980.12841800.10063587376794
1.5398-1.57560.12722000.10353605380595
1.5756-1.6150.12431880.10183631381995
1.615-1.65870.13571960.10583621381795
1.6587-1.70750.12882050.10953664386995
1.7075-1.76260.12881860.11063667385396
1.7626-1.82560.12531690.11293729389896
1.8256-1.89870.14061980.11433676387496
1.8987-1.98510.14142290.11523701393097
1.9851-2.08980.12681970.11483729392697
2.0898-2.22070.12792040.11223760396497
2.2207-2.39220.14231880.11483819400798
2.3922-2.63290.13082120.11993795400798
2.6329-3.01390.15162040.12883856406098
3.0139-3.7970.15432130.13763908412199
3.797-53.46660.15012090.13174085429499

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