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- PDB-2ggn: Conformational mobility in the active site of a heme peroxidase -

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Basic information

Entry
Database: PDB / ID: 2ggn
TitleConformational mobility in the active site of a heme peroxidase
Componentscytosolic ascorbate peroxidase 1
KeywordsOXIDOREDUCTASE / orthogonal bundle
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / 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 / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsBadyal, S.K. / Joyce, M.G. / Sharp, K.H. / Raven, E.L. / Moody, P.C.E.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Conformational Mobility in the Active Site of a Heme Peroxidase.
Authors: Badyal, S.K. / Joyce, M.G. / Sharp, K.H. / Seward, H.E. / Mewies, M. / Basran, J. / Macdonald, I.K. / Moody, P.C.E. / Raven, E.L.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: cytosolic ascorbate peroxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0785
Polymers28,2471
Non-polymers8324
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.672, 81.672, 75.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein cytosolic ascorbate peroxidase 1 / E.C.1.11.1.11


Mass: 28246.775 Da / Num. of mol.: 1 / Mutation: W41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: ascorbate peroxidase / Production host: Escherichia coli (E. coli) / References: UniProt: Q43758, L-ascorbate peroxidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 2.4 M lithium sulphate, 0.1 M HEPES pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.35→28.88 Å / Num. obs: 56193 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 17.8
Reflection shellResolution: 1.35→1.42 Å / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCdata collection
MOSFLMdata reduction
REFMAC5.2refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.35→26.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.622 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20466 2854 5.1 %RANDOM
Rwork0.18967 ---
all0.19042 53286 --
obs0.19042 53286 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.459 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.35→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 54 265 2209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222083
X-RAY DIFFRACTIONr_angle_refined_deg1.0862.0512859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9295272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82924.48387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69715334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.372159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021629
X-RAY DIFFRACTIONr_nbd_refined0.2010.21037
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2188
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.220
X-RAY DIFFRACTIONr_mcbond_it0.7051.51286
X-RAY DIFFRACTIONr_mcangle_it1.21822070
X-RAY DIFFRACTIONr_scbond_it1.7623821
X-RAY DIFFRACTIONr_scangle_it2.7184.5780
X-RAY DIFFRACTIONr_rigid_bond_restr0.99132107
X-RAY DIFFRACTIONr_sphericity_free2.4813267
X-RAY DIFFRACTIONr_sphericity_bonded2.29632016
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 225 -
Rwork0.271 3906 -
obs--99.88 %

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