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- PDB-1bva: MANGANESE BINDING MUTANT IN CYTOCHROME C PEROXIDASE -

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Basic information

Entry
Database: PDB / ID: 1bva
TitleMANGANESE BINDING MUTANT IN CYTOCHROME C PEROXIDASE
ComponentsPROTEIN (CYTOCHROME C PEROXIDASE)
KeywordsOXIDOREDUCTASE / PEROXIDASE / METALLOENZYME / PROTEIN ENGINEERING
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / 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: 1.89 Å
AuthorsWilcox, S.K. / Mcree, D.E. / Goodin, D.B.
CitationJournal: Biochemistry / Year: 1998
Title: Rational design of a functional metalloenzyme: introduction of a site for manganese binding and oxidation into a heme peroxidase.
Authors: Wilcox, S.K. / Putnam, C.D. / Sastry, M. / Blankenship, J. / Chazin, W.J. / McRee, D.E. / Goodin, D.B.
History
DepositionSep 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CYTOCHROME C PEROXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3073
Polymers33,6351
Non-polymers6712
Water6,936385
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.800, 73.600, 50.500
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 PROTEIN (CYTOCHROME C PEROXIDASE) / CCP/MP6.8


Mass: 33635.371 Da / Num. of mol.: 1 / Mutation: D37E,P44D,V45D
Source method: isolated from a genetically manipulated source
Details: CRYSTAL FORM MKTBY
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BL21 (DE3) / Description: MUTATION TO BIND MANGANESE / Cellular location: CYTOPLASM / Gene: CCP (MKT) / Organelle: MITOCHONDRIA / Plasmid: PT7CCP / Species (production host): Escherichia coli / 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#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.: 385 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CYTOCHROME C PEROXIDASE DIFFERS FROM 2CYP BY STRAIN RELATED SUBSTITUTIONS OF THR 53 WITH ILE, ...THIS CYTOCHROME C PEROXIDASE DIFFERS FROM 2CYP BY STRAIN RELATED SUBSTITUTIONS OF THR 53 WITH ILE, ASP 152 WITH GLY. THE N-TERMINUS HAS THREE RESIDUES MET-LYS-THR WHICH ARE NOT OBSERVED IN THE CRYSTAL STRUCTURE. IN THIS REGARD IT DIFFERS SLIGHTLY FROM THE CCP IN ENTRIES 2CCP, 3CCP, 4CCP. ASP 37 HAS BEEN REPLACED BY GLU, PRO 44 HAS BEEN REPLACED BY ASP, AND VAL 45 HAS BEEN REPLACED BY ASP.

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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 %
Description: A 100K STRUCTURE OF 1CCG WAS USED INITIALLY BECAUSE IT HAD THE MOST SIMILAR UNIT CELL. THE APPROPRIATE AMINO ACID IDENTITIES WERE CHANGED.
Crystal growpH: 6 / Details: 20% MPD, 35 MM PHOSPHATE, PH 6.0, 5 MM MNSO4.
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.17 mMprotein1drop
215 mMpotassium phosphate1drop
35 mM1dropMnSO4
410 %MPD1drop
525 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→15 Å / Num. obs: 26232 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 18.8
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.39 / Rsym value: 0.14 / % possible all: 42

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Processing

Software
NameClassification
SHELXL-97refinement
XTALVIEWrefinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CCG

1ccg


Resolution: 1.89→10 Å / Num. parameters: 10891 / Num. restraintsaints: 9784 / σ(F): 2
RfactorNum. reflection% reflection
obs0.179 -81 %
all-25534 -
Refinement stepCycle: LAST / Resolution: 1.89→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 44 385 2738
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d1.7
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor all: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 1.7

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