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

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Basic information

Entry
Database: PDB / ID: 1aef
TitleSPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACTIVE SITE OF CYTOCHROME C PEROXIDASE (3-AMINOPYRIDINE)
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 / 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
3-AMINOPYRIDINE / PROTOPORPHYRIN IX CONTAINING FE / 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 24, 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 1.3Nov 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 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 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
Water1,820101
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-3AP / 3-AMINOPYRIDINE


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.: 101 / 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 3-AMINOPYRIDINE 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 RUH2R / 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: 23265 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.087 / Net I/σ(I): 11.94
Reflection shellResolution: 2.03→2.18 Å / Redundancy: 1.68 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.51 / Rsym value: 0.54 / % possible all: 79
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.087

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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
Details: THE PROTEIN AND WATER COORDINATES WERE TAKEN FROM PDB ENTRY 1AA4. THE LIGAND COORDINATES WERE MEASURED FROM THE OMIT MAP. NO REFINEMENT WAS CARRIED OUT ON THE RESULTING SET OF COORDINATES, ...Details: THE PROTEIN AND WATER COORDINATES WERE TAKEN FROM PDB ENTRY 1AA4. THE LIGAND COORDINATES WERE MEASURED FROM THE OMIT MAP. NO REFINEMENT WAS CARRIED OUT ON THE RESULTING SET OF COORDINATES, WHICH ARE THE COORDINATES PRESENTED IN THIS ENTRY.
Num. reflection% reflection
obs19099 79 %
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 57 101 2999

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