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- PDB-5ug2: CcP gateless cavity -

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Basic information

Entry
Database: PDB / ID: 5ug2
TitleCcP gateless cavity
ComponentsPeroxidase
KeywordsOXIDOREDUCTASE / Model system / Cytochrome c Peroxidase / GIST / water / 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
6-fluoro-2-methylimidazo[1,2-a]pyridin-3-amine / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.34 Å
AuthorsStein, R.M. / Fischer, 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
DepositionJan 6, 2017Deposition 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

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Assembly

Deposited unit
A: Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7103
Polymers32,9291
Non-polymers7822
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.309, 72.848, 104.410
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 / Fragment: UNP RESIDUES 72-362 / 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
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Chemical ChemComp-86J / 6-fluoro-2-methylimidazo[1,2-a]pyridin-3-amine


Mass: 165.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8FN3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.91 Å3/Da / Density % sol: 57.73 % / 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: 1.34→59.744 Å / Num. obs: 87297 / % possible obs: 98.5 % / Redundancy: 11.1 % / Biso Wilson estimate: 16.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.34-1.375.41.1080.695184.7
5.99-59.7411.70.0241199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.63 Å59.74 Å
Translation6.63 Å59.74 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: 1.34→59.744 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.76
RfactorNum. reflection% reflection
Rfree0.1743 4320 5.03 %
Rwork0.1542 --
obs0.1552 85804 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.71 Å2 / Biso mean: 23.7019 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: final / Resolution: 1.34→59.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 20 397 2788
Biso mean--20.07 35.31 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072493
X-RAY DIFFRACTIONf_angle_d1.0673393
X-RAY DIFFRACTIONf_chiral_restr0.061329
X-RAY DIFFRACTIONf_plane_restr0.005448
X-RAY DIFFRACTIONf_dihedral_angle_d14.834905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.34-1.35520.5475870.4643171662
1.3552-1.37120.37121160.3835214978
1.3712-1.38790.40441150.3349244688
1.3879-1.40550.34231360.2924257994
1.4055-1.4240.31511460.2719270997
1.424-1.44350.29771380.2431275399
1.4435-1.46410.24851500.22052780100
1.4641-1.4860.22781290.21222767100
1.486-1.50920.23511700.21422761100
1.5092-1.53390.24121620.19822748100
1.5339-1.56040.22941560.19172752100
1.5604-1.58880.21011390.18782786100
1.5888-1.61930.19211330.18862775100
1.6193-1.65240.22191410.17042812100
1.6524-1.68830.20141470.1703272299
1.6883-1.72760.19951420.1582276399
1.7276-1.77080.20481550.1612276799
1.7708-1.81870.17521550.1594277499
1.8187-1.87220.18961590.1552273899
1.8722-1.93260.17771510.1557275999
1.9326-2.00170.15431430.1511277699
2.0017-2.08180.18291570.1417280299
2.0818-2.17660.15081480.1379278999
2.1766-2.29140.18441440.1323280099
2.2914-2.43490.14371420.1326280899
2.4349-2.62290.16071620.13332818100
2.6229-2.88690.1551440.13832829100
2.8869-3.30460.14221540.14092857100
3.3046-4.16330.14671380.13352917100
4.1633-59.7440.14491610.14063032100

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