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- PDB-4atj: DISTAL HEME POCKET MUTANT (H42E) OF RECOMBINANT HORSERADISH PEROX... -

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Basic information

Entry
Database: PDB / ID: 4atj
TitleDISTAL HEME POCKET MUTANT (H42E) OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID
ComponentsPROTEIN (PEROXIDASE C1A)
KeywordsOXIDOREDUCTASE / PEROXIDASE / HEME ENZYME / MUTANT
Function / homology
Function and homology information


peroxidase / lactoperoxidase activity / vacuole / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Plant peroxidase / Secretory peroxidase / 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 ...Plant peroxidase / Secretory peroxidase / 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
BENZHYDROXAMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesArmoracia rusticana (horseradish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMeno, K. / Jennings, S. / Smith, A.T. / Henriksen, A. / Gajhede, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structural analysis of the two horseradish peroxidase catalytic residue variants H42E and R38S/H42E: implications for the catalytic cycle.
Authors: Meno, K. / Jennings, S. / Smith, A.T. / Henriksen, A. / Gajhede, M.
#1: Journal: Biochemistry / Year: 1998
Title: Structural interactions between horseradish peroxidase C and the substrate benzhydroxamic acid determined by X-ray crystallography.
Authors: Henriksen, A. / Schuller, D.J. / Meno, K. / Welinder, K.G. / Smith, A.T. / Gajhede, M.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of horseradish peroxidase C at 2.15 A resolution.
Authors: Gajhede, M. / Schuller, D.J. / Henriksen, A. / Smith, A.T. / Poulos, T.L.
History
DepositionApr 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 27, 2019Group: Database references / Derived calculations / Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 25, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PEROXIDASE C1A)
B: PROTEIN (PEROXIDASE C1A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,80810
Polymers68,1412
Non-polymers1,6688
Water5,477304
1
A: PROTEIN (PEROXIDASE C1A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9045
Polymers34,0701
Non-polymers8344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PEROXIDASE C1A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9045
Polymers34,0701
Non-polymers8344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.930, 62.270, 78.230
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.0063, 0.0026), (0.0063, -1, 0.0072), (0.0026, 0.0072, 1)
Vector: 18.0698, 29.6212, 0.0409)

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Components

#1: Protein PROTEIN (PEROXIDASE C1A) / HRP C / HRP C1A


Mass: 34070.309 Da / Num. of mol.: 2 / Mutation: H42E
Source method: isolated from a genetically manipulated source
Details: CONTAINS HEME, TWO STRUCTURAL CALCIUM IONS, AND BENZHYDROXAMIC ACID BOUND IN ACTIVE SITE
Source: (gene. exp.) Armoracia rusticana (horseradish) / Production host: Escherichia coli (E. coli) / References: UniProt: P00433, peroxidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-BHO / BENZHYDROXAMIC ACID


Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE CHARGE IS UNKNOWN SINCE IT IS POSITIONED IN THE ACTIVE SITE, WHICH CHANGES THE NORMAL PKA. THE ...THE CHARGE IS UNKNOWN SINCE IT IS POSITIONED IN THE ACTIVE SITE, WHICH CHANGES THE NORMAL PKA. THE CHARGE OF 3+ REFERS TO THE FE ATOM. THE CARBOXYLIC ACIDS AND THE NITROGENS WILL CONTRIBUTE SOME NEGATIVE CHARGE TO THE OVERALL VALUE.
Sequence detailsTHE N-TERMINAL METHIONINE ORIGINATES FROM THE E. COLI EXPRESSION SYSTEM. RESIDUES 1 - 29 AND 339 - ...THE N-TERMINAL METHIONINE ORIGINATES FROM THE E. COLI EXPRESSION SYSTEM. RESIDUES 1 - 29 AND 339 - 353 DESCRIBED IN SWS ARE PROPEPTIDES. THE FIRST RESIDUE IS NUMBERED ZERO SUCH THAT THE RESIDUE NUMBERS CONFORMS WITH THE WILD TYPE (PDB ENTRY 1ATJ AND 2ATJ).

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 283 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15.7 mg/mlH42E1drop
22.5 mMBHA1reservoir
31.2 M1reservoirNH4H2PO4
40.1 Mcacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 23291 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3 / % possible all: 95.4
Reflection
*PLUS
Lowest resolution: 45 Å / Num. obs: 23302 / % possible obs: 95.4 % / Redundancy: 3.4 % / Num. measured all: 79639
Reflection shell
*PLUS
% possible obs: 95.4 % / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ATJ

2atj


Resolution: 2.5→45 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE STRUCTURE WAS REFINED USING STRICT NON- CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2235 9.8 %RANDOM
Rwork0.162 ---
obs-22747 93.2 %-
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 110 304 5184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.031.5
X-RAY DIFFRACTIONx_mcangle_it3.052
X-RAY DIFFRACTIONx_scbond_it3.692
X-RAY DIFFRACTIONx_scangle_it5.162.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.5→2.54 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 115 10.6 %
Rwork0.224 970 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_KM.PARAMTOPHCSDX_KM.PRO
X-RAY DIFFRACTION2PARAM19X_KM_CF_N.HEMETOPH19X_KM_CF_N.HEME
X-RAY DIFFRACTION3PARAMETER_KM.ELEMENTSTOPH_NOCHARGE.MG
X-RAY DIFFRACTION4PARAM19.SOLTOPH19_KM.SOL
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 45 Å / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.94

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