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- PDB-5u5z: CcP gateless cavity -

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Basic information

Entry
Database: PDB / ID: 5u5z
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
4-methyl-2-phenyl-1H-imidazole / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.26 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)33,7033
Polymers32,9291
Non-polymers7752
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.251, 73.239, 104.829
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-7VP / 4-methyl-2-phenyl-1H-imidazole


Mass: 158.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.93 Å3/Da / Density % sol: 58.08 % / 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: 1.26→73.24 Å / Num. obs: 90514 / % possible obs: 84.7 % / Redundancy: 11.3 % / Biso Wilson estimate: 14.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Net I/σ(I): 14.8 / Num. measured all: 1022444 / Scaling rejects: 460
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.26-1.295.60.7390.802130.6
5.64-73.2411.60.031199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.64 Å52.41 Å
Translation6.64 Å52.41 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: 1.26→52.414 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.68
RfactorNum. reflection% reflection
Rfree0.1664 4552 5.04 %
Rwork0.1408 --
obs0.1421 90360 84.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.32 Å2 / Biso mean: 20.3868 Å2 / Biso min: 9.13 Å2
Refinement stepCycle: final / Resolution: 1.26→52.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 22 293 2686
Biso mean--25.76 27.73 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122549
X-RAY DIFFRACTIONf_angle_d1.3463472
X-RAY DIFFRACTIONf_chiral_restr0.089335
X-RAY DIFFRACTIONf_plane_restr0.008463
X-RAY DIFFRACTIONf_dihedral_angle_d14.373935
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 (%)
1.26-1.27440.3355380.288887791526
1.2744-1.28940.3509560.29021066112232
1.2894-1.30510.313700.26971274134438
1.3051-1.32160.3038870.25041531161846
1.3216-1.3390.2783960.21551688178450
1.339-1.35730.24091010.20851899200056
1.3573-1.37670.27441040.18792147225164
1.3767-1.39730.25971190.18852368248770
1.3973-1.41910.2351350.18452656279179
1.4191-1.44240.19471760.17942948312489
1.4424-1.46730.1851640.16963262342696
1.4673-1.49390.19751980.15613237343598
1.4939-1.52270.21971700.15013288345898
1.5227-1.55380.18051790.1483283346297
1.5538-1.58750.16651910.14363298348999
1.5875-1.62450.17041980.13883295349398
1.6245-1.66510.17531890.13363289347898
1.6651-1.71010.17621720.12893323349598
1.7101-1.76040.15861700.12843354352499
1.7604-1.81730.16461740.12943357353199
1.8173-1.88220.1581720.13473385355799
1.8822-1.95760.17461780.13623341351999
1.9576-2.04670.14451630.13843375353899
2.0467-2.15460.16361690.13233402357199
2.1546-2.28960.16321780.123634073585100
2.2896-2.46640.16791840.130934073591100
2.4664-2.71460.16081590.135134623621100
2.7146-3.10730.16261870.141834393626100
3.1073-3.91470.1561930.139534903683100
3.9147-52.45990.13731820.135536603842100

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