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- PDB-5u5u: CcP gateless cavity -

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Basic information

Entry
Database: PDB / ID: 5u5u
TitleCcP gateless cavity
ComponentsPeroxidase
KeywordsOXIDOREDUCTASE / Model system / Cytochrome c Peroxidase / water / GIST / desolvation / 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
PROTOPORPHYRIN IX CONTAINING FE / ISONICOTINAMIDINE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.33 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

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Assembly

Deposited unit
A: Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6663
Polymers32,9291
Non-polymers7382
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.007, 74.920, 106.941
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 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NTN / ISONICOTINAMIDINE


Mass: 121.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 3.1 Å3/Da / Density % sol: 60.38 % / 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 5, 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: 1.3→61.36 Å / Num. obs: 93829 / % possible obs: 93.1 % / Redundancy: 11.1 % / Biso Wilson estimate: 15.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.3-1.335.41.1910.701159.8
5.81-50.9711.60.0390.999199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.68 Å61.36 Å
Translation6.68 Å61.36 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: 1.33→61.36 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.35
RfactorNum. reflection% reflection
Rfree0.1923 4423 4.95 %
Rwork0.172 --
obs0.173 89439 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.49 Å2 / Biso mean: 20.895 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 1.33→61.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 16 333 2720
Biso mean--14.92 29.74 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092507
X-RAY DIFFRACTIONf_angle_d1.1623410
X-RAY DIFFRACTIONf_chiral_restr0.07332
X-RAY DIFFRACTIONf_plane_restr0.006452
X-RAY DIFFRACTIONf_dihedral_angle_d14.12915
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.33-1.34510.357840.35187462
1.3451-1.36090.36731170.3398198668
1.3609-1.37750.34631090.3231216773
1.3775-1.3950.34551240.3072235879
1.395-1.41330.33391140.3252985
1.4133-1.43270.30921480.283274994
1.4327-1.45320.31711310.2699291297
1.4532-1.47490.29281440.2602288799
1.4749-1.49790.24171410.2538296198
1.4979-1.52250.28011370.2412293699
1.5225-1.54870.24021670.2421289898
1.5487-1.57690.23571550.2287294999
1.5769-1.60720.26611440.2223292498
1.6072-1.640.23461600.2191292999
1.64-1.67570.24071770.224291298
1.6757-1.71470.21941440.2079294198
1.7147-1.75760.27011530.201296099
1.7576-1.80510.25831330.1956296299
1.8051-1.85820.1911490.1892295198
1.8582-1.91820.2121620.1903295799
1.9182-1.98670.22141810.1754292198
1.9867-2.06630.19911520.165297899
2.0663-2.16030.17481610.1601297299
2.1603-2.27420.16261670.1528299199
2.2742-2.41670.16821450.1565301599
2.4167-2.60330.17431650.1552297499
2.6033-2.86530.15451710.1523302199
2.8653-3.27990.18721590.14743061100
3.2799-4.13220.1441590.13493101100
4.1322-61.360.1571700.13633240100

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