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- PDB-1jci: Stabilization of the Engineered Cation-binding Loop in Cytochrome... -

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Basic information

Entry
Database: PDB / ID: 1jci
TitleStabilization of the Engineered Cation-binding Loop in Cytochrome c Peroxidase (CcP)
ComponentsCytochrome C Peroxidase
KeywordsOXIDOREDUCTASE / Cation-binding loop / Trp191 cationic radical / open/closed conformer
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 / : / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBhaskar, B. / Bonagura, C.A. / Li, H. / Poulos, T.L.
Citation
Journal: Biochemistry / Year: 2002
Title: Cation-induced stabilization of the engineered cation-binding loop in cytochrome c peroxidase (CcP).
Authors: Bhaskar, B. / Bonagura, C.A. / Li, H. / Poulos, T.L.
#1: Journal: Biochemistry / Year: 1999
Title: The Effects of an Engineered Cation Site on the Structure, Activity and EPR Properties of Cytochrome C Peroxidase
Authors: Bonagura, C.A. / Sundaramoorthy, M. / Bhaskar, B. / Poulos, T.L.
#2: Journal: Biochemistry / Year: 1996
Title: An Engineered Cation Site in Cytochrome C Peroxidase Alters the Reactivity of the Redox Active Tryptophan
Authors: Bonagura, C.A. / Sundaramoorthy, M. / Pappa, H.S. / Patterson, W.R. / Poulos, T.L.
History
DepositionJun 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Oct 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 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)34,2993
Polymers33,6431
Non-polymers6562
Water13,151730
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.680, 75.340, 51.300
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


Mass: 33643.305 Da / Num. of mol.: 1 / Mutation: A176T, G192T, A194N, N195P, T199D, E201S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cellular location: mitochondrial matrix / 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 / Heme B


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


Mass: 18.015 Da / Num. of mol.: 730 / 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: 59.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-Methyl-2,4-Pentanediol, potassium phosphate, pH 6.0, vapor diffusion, sitting drop, temperature 277K
Crystal grow
*PLUS
Method: unknown
Details: Sundaramoorthy, M., (1991) J.Am.Chem.Soc., 113, 7755.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein11
20.05 Mpotassium phosphate12pH6.0
325 %MPD12

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Data collection

DiffractionMean temperature: 116 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 315272 / Num. obs: 33299 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.1969112 / Num. unique all: 1622 / Rsym value: 0.396 / % possible all: 99.5
Reflection
*PLUS
% possible obs: 99.4 % / Num. measured all: 315272
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: calcium binding CcP

Resolution: 1.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 1154 -random
Rwork0.1582 ---
all-33299 --
obs-33299 100 %-
Refine analyze
ObsFree
Luzzati coordinate error0.15 Å-
Luzzati d res low5 Å-
Luzzati sigma a0.16 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 44 730 3167
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005127
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.25233
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.9-1.970.23851310.2175X-RAY DIFFRACTION28566
1.97-2.050.24281720.1943X-RAY DIFFRACTION28876
2.05-2.140.21991590.1181X-RAY DIFFRACTION29916
2.14-2.250.24151640.1736X-RAY DIFFRACTION30006
3.25-4.090.16631840.1342X-RAY DIFFRACTION31616
4.09-500.1861750.1469X-RAY DIFFRACTION32916
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / Rfactor obs: 0.1582
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.2175

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