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- PDB-3zch: Ascorbate peroxidase W41A-H42M mutant -

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Basic information

Entry
Database: PDB / ID: 3zch
TitleAscorbate peroxidase W41A-H42M mutant
ComponentsASCORBATE PEROXIDASE
KeywordsOXIDOREDUCTASE / CONFORMATIONAL MOBILITY
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / cellular response to oxidative stress / heme binding / 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 / : / L-ascorbate peroxidase
Similarity search - Component
Biological speciesGLYCINE MAX (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGumiero, A. / Raven, E.L. / Moody, P.C.E.
CitationJournal: Dalton Trans / Year: 2013
Title: Probing the Conformational Mobility of the Active Site of Ascorbate Peroxidase
Authors: Guimero, A. / Badyal, S.K. / Leeks, T. / Moody, P.C.E. / Raven, E.L.
History
DepositionNov 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5647
Polymers28,2401
Non-polymers1,3246
Water4,702261
1
A: ASCORBATE PEROXIDASE
hetero molecules

A: ASCORBATE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,12814
Polymers56,4802
Non-polymers2,64912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area4990 Å2
ΔGint-85.4 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.629, 82.629, 74.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

21A-2232-

HOH

31A-2233-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ASCORBATE PEROXIDASE / / CYTOSOLIC ASCORBATE PEROXIDASE 1


Mass: 28239.822 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-250 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GLYCINE MAX (soybean) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: Q43758, L-ascorbate peroxidase

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Non-polymers , 5 types, 267 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 1.99 Å3/Da / Density % sol: 37.76 % / Description: NONE
Crystal growpH: 8.5 / Details: LISO4 2.5M, HEPES 100 MM PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→82.76 Å / Num. obs: 18087 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.52 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.61

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAF

1oaf


Resolution: 2→46.08 Å / SU ML: 0.17 / σ(F): 1.39 / Phase error: 16.24 / Stereochemistry target values: ML
Details: PREVIOUS REFINEMENT CYCLES WERE CARRIED OUT WITH REFMAC 5.0. THERE IS ONE DISORDERED REGION IN THE STRUCTURE, BETWEEN RESIDUES 65 AND 70. THIS REGION WAS MODELLED ON THE FO-FC MAP, ...Details: PREVIOUS REFINEMENT CYCLES WERE CARRIED OUT WITH REFMAC 5.0. THERE IS ONE DISORDERED REGION IN THE STRUCTURE, BETWEEN RESIDUES 65 AND 70. THIS REGION WAS MODELLED ON THE FO-FC MAP, CALCULATED WHEN THE OCCUPANCY OF RESIDUES WAS SET TO 0.
RfactorNum. reflection% reflection
Rfree0.1985 919 5.1 %
Rwork0.1529 --
obs0.1551 18061 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 72 261 2227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072062
X-RAY DIFFRACTIONf_angle_d1.2432816
X-RAY DIFFRACTIONf_dihedral_angle_d14.66769
X-RAY DIFFRACTIONf_chiral_restr0.088290
X-RAY DIFFRACTIONf_plane_restr0.005368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10540.1971340.14312410X-RAY DIFFRACTION100
2.1054-2.23740.21971240.14222407X-RAY DIFFRACTION100
2.2374-2.41010.17891340.14332393X-RAY DIFFRACTION100
2.4101-2.65260.21461380.15172429X-RAY DIFFRACTION100
2.6526-3.03640.20141240.16752447X-RAY DIFFRACTION100
3.0364-3.82520.20871280.15112477X-RAY DIFFRACTION100
3.8252-46.09230.18331370.15742579X-RAY DIFFRACTION98

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