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- PDB-3atj: HEME LIGAND MUTANT OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 3atj
TitleHEME LIGAND MUTANT OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID
ComponentsPROTEIN (HORSERADISH 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: 2.2 Å
AuthorsMeno, K. / White, C.G. / Smith, A.T. / Gajhede, M.
Citation
Journal: To be Published
Title: Structural and Catalytical Implications of a F221M Mutation in the Proximal Pocket of Horseradish Peroxidase C (HRP C)
Authors: Meno, K. / White, C.G. / Smith, A.T. / 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
DepositionDec 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 28, 1999Provider: 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 1.4Aug 30, 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_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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,79410
Polymers68,1272
Non-polymers1,6688
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.105, 62.283, 78.160
Angle α, β, γ (deg.)90.00, 104.31, 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 (HORSERADISH PEROXIDASE C1A) / HRP C / HRP C1A


Mass: 34063.363 Da / Num. of mol.: 2 / Mutation: F221M
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.: 364 / 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.

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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: 52.8 %
Crystal growpH: 6.5 / Details: pH 6.5

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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: Jun 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: 2.2→50 Å / Num. obs: 32731 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3 / % possible all: 92.1

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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: 2.2→50 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
Rfree0.203 3247 10 %RANDOM
Rwork0.174 ---
obs-32424 90.7 %-
Displacement parametersBiso mean: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4750 0 110 364 5224
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_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.89
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.71.5
X-RAY DIFFRACTIONx_mcangle_it2.422
X-RAY DIFFRACTIONx_scbond_it3.42
X-RAY DIFFRACTIONx_scangle_it4.812.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.2→2.24 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 138 9.9 %
Rwork0.229 1252 -
obs--78.3 %
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

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