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- PDB-1krj: Engineering Calcium-binding site into Cytochrome c Peroxidase (CcP) -

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Basic information

Entry
Database: PDB / ID: 1krj
TitleEngineering Calcium-binding site into Cytochrome c Peroxidase (CcP)
ComponentsCytochrome c Peroxidase
KeywordsOXIDOREDUCTASE / Cation-binding loop / Calcium selectivity / Trp191 cationic-radical / open/closed conformer / bidentate bond / pentagonal bipyrimidal geometry / lignin peroxidase
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
PROTOPORPHYRIN IX CONTAINING FE / : / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBonagura, C.A. / Bhaskar, B. / Sundaramoorthy, M. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Conversion of an engineered potassium-binding site into a calcium-selective site in cytochrome c peroxidase.
Authors: Bonagura, C.A. / Bhaskar, B. / Sundaramoorthy, M. / Poulos, T.L.
History
DepositionJan 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 400COMPOUND Largely a helical bundle protein containing a distinct distal and proximal heme domains. ...COMPOUND Largely a helical bundle protein containing a distinct distal and proximal heme domains. Proximal heme domain contains the cation-binding loop which in the present case contains Calcium coordinated by the residues 190-199 of the loop.

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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)34,3173
Polymers33,6611
Non-polymers6562
Water10,791599
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.034, 75.458, 51.100
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsLargely a helical bundle protein containing a distinct distal and proximal heme domains. Proximal heme domian contains the cation-binding loop which in the present case contains Calcium coordinated by the residues 190-199 of the loop

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Components

#1: Protein Cytochrome c Peroxidase / CCP


Mass: 33661.277 Da / Num. of mol.: 1 / Fragment: Proximal Cation-binding Loop / Mutation: A176T, G192D, A194T, T199D, E201S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OPBYC / Plasmid: pT7CcP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-Methyl-2,4-Pentanediol (MPD), potassium phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTrizma1dropTris base
250 mMacetic acid1drop
350 mMMES1droppH6.0
430 %MPD1reservoir
52 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 29, 1998 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 28764 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8627 % / Rmerge(I) obs: 0.082 / Rsym value: 0.057 / Net I/σ(I): 19.2082
Reflection shellResolution: 2→2.02 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3023 / Num. unique all: 706 / Rsym value: 0.354 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 28701 / % possible obs: 99.8 % / Num. measured all: 155672
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Potassium-binding CcP (CcPK2)

Resolution: 2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rwork0.192 ---
Rfree-1645 -RANDOM
obs-25912 100 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 44 599 3049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.32
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
2-2.090.1921X-RAY DIFFRACTION2712
2.09-2.20.1871X-RAY DIFFRACTION2956
2.2-2.340.1821X-RAY DIFFRACTION3141
2.34-2.510.1775X-RAY DIFFRACTION3217
2.51-2.760.1728X-RAY DIFFRACTION3334
2.76-3.150.1683X-RAY DIFFRACTION3403
3.15-3.930.166X-RAY DIFFRACTION3506
3.93-100.1762X-RAY DIFFRACTION3643
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d

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