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- PDB-5u5y: CcP gateless cavity -

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Basic information

Entry
Database: PDB / ID: 5u5y
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
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: 1.3 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)33,6923
Polymers32,9291
Non-polymers7642
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.260, 74.663, 106.937
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-7W4 / 2-methylimidazo[1,2-a]pyridin-3-amine


Mass: 147.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3.05 Å3/Da / Density % sol: 59.7 % / 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: 1.3→74.66 Å / Num. obs: 93112 / % possible obs: 91.6 % / Redundancy: 11.3 % / Biso Wilson estimate: 13.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.018 / Rrim(I) all: 0.063 / Net I/σ(I): 16.6 / Num. measured all: 1054450 / Scaling rejects: 1146
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.3-1.3360.90.735152.8
5.81-74.6611.70.0231199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.68 Å46.22 Å
Translation6.68 Å46.22 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: 1.3→46.223 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.85
RfactorNum. reflection% reflection
Rfree0.1933 4651 5.04 %
Rwork0.1641 --
obs0.1655 92343 90.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.29 Å2 / Biso mean: 19.5476 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 1.3→46.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 11 331 2713
Biso mean--16.6 29.51 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132563
X-RAY DIFFRACTIONf_angle_d1.3713492
X-RAY DIFFRACTIONf_chiral_restr0.067337
X-RAY DIFFRACTIONf_plane_restr0.008464
X-RAY DIFFRACTIONf_dihedral_angle_d14.132938
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 (%)
1.3-1.31480.4028700.40731503157347
1.3148-1.33020.3765860.38391606169251
1.3302-1.34650.36791010.33911818191957
1.3465-1.36350.41991050.33482005211063
1.3635-1.38150.33991140.30662207232170
1.3815-1.40040.3391210.28092421254276
1.4004-1.42040.28611280.26692630275883
1.4204-1.44160.31041760.25352803297989
1.4416-1.46410.28471660.22013195336199
1.4641-1.48810.26441720.206831303302100
1.4881-1.51380.23591500.19832033353100
1.5138-1.54130.22991740.187431653339100
1.5413-1.5710.22051750.184231703345100
1.571-1.6030.21271550.175932093364100
1.603-1.63790.20731740.178231683342100
1.6379-1.6760.21671940.167831863380100
1.676-1.71790.20831610.158931953356100
1.7179-1.76440.18451690.161131903359100
1.7644-1.81630.20671390.161832333372100
1.8163-1.87490.19371730.16283169334299
1.8749-1.94190.21391770.16063171334899
1.9419-2.01970.19651750.156432103385100
2.0197-2.11160.16591860.14933182336899
2.1116-2.22290.16441740.14833212338699
2.2229-2.36220.17241490.15183213336299
2.3622-2.54450.19761820.15283225340799
2.5445-2.80060.18691830.16243227341099
2.8006-3.20570.17251660.15532723438100
3.2057-4.03850.16461780.141632913469100
4.0385-46.25270.15351780.136134833661100

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