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- PDB-5l86: engineered ascorbate peroxidise -

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Basic information

Entry
Database: PDB / ID: 5l86
Titleengineered ascorbate peroxidise
ComponentsAscorbate peroxidase
KeywordsOXIDOREDUCTASE / protein engineering / peroxidase / heme / apx2 / methyl histidine
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: 1.9 Å
AuthorsHayashi, T. / Mittl, P. / Hilvert, D.
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: A Chemically Programmed Proximal Ligand Enhances the Catalytic Properties of a Heme Enzyme.
Authors: Green, A.P. / Hayashi, T. / Mittl, P.R. / Hilvert, D.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ascorbate peroxidase
B: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,43810
Polymers53,6282
Non-polymers1,8098
Water6,936385
1
A: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7195
Polymers26,8141
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7195
Polymers26,8141
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.460, 81.950, 69.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 3 - 249 / Label seq-ID: 1 - 247

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ascorbate peroxidase / / Cytosolic ascorbate peroxidase 1


Mass: 26814.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MHS: N(delta)-methyl histidine / Source: (gene. exp.) Glycine max (soybean) / Gene: apx1, GLYMA_U021900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43758, L-ascorbate peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM bis-tris, pH 5.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→60 Å / Num. obs: 73768 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 31.798 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.353 / Net I/σ(I): 4.73
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-1.953.6880.561100
1.95-22.8050.751100
2-2.11.8691.151100
2.1-2.251.4221.551100
2.25-2.50.952.371100
2.5-30.5514.071100
3-40.1889.421100
4-50.10915.821100
5-60.117151100
60.08418.26199.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1v0h

1v0h


Resolution: 1.9→58.81 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.049 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1910 4.9 %RANDOM
Rwork0.1794 ---
obs0.1819 36931 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.87 Å2 / Biso mean: 30.877 Å2 / Biso min: 14.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å2-0 Å2
2---0.34 Å20 Å2
3---0.91 Å2
Refinement stepCycle: final / Resolution: 1.9→58.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 116 385 4289
Biso mean--32.99 38.2 -
Num. residues----494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194014
X-RAY DIFFRACTIONr_angle_refined_deg1.8182.0265474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74924.286168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03715620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2951518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0223110
X-RAY DIFFRACTIONr_mcbond_it1.1322.0871974
X-RAY DIFFRACTIONr_mcangle_it1.8723.1242464
X-RAY DIFFRACTIONr_scbond_it1.552.242040
Refine LS restraints NCS

Ens-ID: 1 / Number: 648 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 122 -
Rwork0.35 2687 -
all-2809 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.86770.12150.0831.2468-0.22520.9165-0.0014-0.0242-0.07650.00070.08680.19850.0233-0.1153-0.08540.0044-0.00540.01450.02110.01420.1247-6.649-5.389412.5543
22.17880.2481-0.15761.01410.03670.65450.0620.22550.1363-0.094-0.04730.06180.0146-0.0279-0.01480.01550.02-0.00370.0457-0.00050.05529.47162.8839-16.6336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 249
2X-RAY DIFFRACTION2B3 - 249

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