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- PDB-1aej: SPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACT... -

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Entry
Database: PDB / ID: 1aej
TitleSPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACTIVE SITE OF CYTOCHROME C PEROXIDASE (1-VINYLIMIDAZOLE)
ComponentsCYTOCHROME C PEROXIDASE
KeywordsOXIDOREDUCTASE / PEROXIDASE / TRANSIT PEPTIDE
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / 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 / 1-VINYLIMIDAZOLE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMusah, R.A. / Jensen, G.M. / Fitzgerald, M.M. / Mcree, D.E. / Goodin, D.B.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein.
Authors: Musah, R.A. / Jensen, G.M. / Bunte, S.W. / Rosenfeld, R.J. / Goodin, D.B.
#1: Journal: Biochemistry / Year: 1994
Title: Small Molecule Binding to an Artificially Created Cavity at the Active Site of Cytochrome C Peroxidase
Authors: Fitzgerald, M.M. / Churchill, M.J. / Mcree, D.E. / Goodin, D.B.
#2: Journal: Biochemistry / Year: 1993
Title: The Asp-His-Fe Triad of Cytochrome C Peroxidase Controls the Reduction Potential, Electronic Structure, and Coupling of the Tryptophan Free Radical to the Heme
Authors: Goodin, D.B. / Mcree, D.E.
History
DepositionFeb 25, 1997Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1713
Polymers33,4591
Non-polymers7122
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.000, 77.300, 51.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C PEROXIDASE / CCP/W191G


Mass: 33459.242 Da / Num. of mol.: 1 / Mutation: W191G
Source method: isolated from a genetically manipulated source
Details: CRYSTAL FORM BY
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: BL21 / Cellular location: MITOCHONDRIA / Gene: CCP / Organelle: MITOCHONDRIA / Plasmid: PT7CCP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): CCP (MKT) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#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-NVI / 1-VINYLIMIDAZOLE


Mass: 95.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growpH: 6
Details: 20% MPD, 40 MM PHOSPHATE PH 6.0. A SINGLE CRYSTAL OF W191G WAS SOAKED IN 50MM 1-VINYLIMIDAZOLE, 5MM ETHANOL, IN 40% MPD AND 60 MM PHOSPHATE AT PH 4.5.
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.5 %(v/v)MPD1drop
2200 mMMES1drop
325 %MPD1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 23913 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 1.85 % / Rmerge(I) obs: 0.087 / Rsym value: 0.085 / Net I/σ(I): 8.44
Reflection shellResolution: 2.01→2.14 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.77 / % possible all: 71
Reflection
*PLUS
Num. obs: 22158 / Rmerge(I) obs: 0.085

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Processing

Software
NameClassification
XTALVIEWrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AA4

1aa4


Resolution: 2.1→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.5 / σ(F): 0 /
Num. reflection% reflection
obs19099 79 %
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 57 100 2998

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