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

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Basic information

Entry
Database: PDB / ID: 2ghd
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 / 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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / L-ascorbate peroxidase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 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 27, 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_asym_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_asym_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_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)28,9854
Polymers28,2471
Non-polymers7393
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.293, 82.293, 75.666
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
11X-9385-

HOH

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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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1 M HEPES, pH 8.3, 2.25 M Lithium Sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315 / 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: 1.4→36.81 Å / Num. obs: 52940 / % possible obs: 92.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.4→1.436 Å / Rmerge(I) obs: 0.088 / % possible all: 96.6

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Processing

Software
NameVersionClassification
ADSCdata collection
MOSFLMdata reduction
REFMAC5.2refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→36.81 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.834 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22949 2622 5.1 %RANDOM
Rwork0.20581 ---
obs0.20701 48714 99.36 %-
all-48714 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.744 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 50 243 2189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222043
X-RAY DIFFRACTIONr_angle_refined_deg1.112.0472790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7615259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00724.36887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70315323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.516159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021591
X-RAY DIFFRACTIONr_nbd_refined0.2060.2921
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.217
X-RAY DIFFRACTIONr_mcbond_it0.8581.51297
X-RAY DIFFRACTIONr_mcangle_it1.35722018
X-RAY DIFFRACTIONr_scbond_it1.9413840
X-RAY DIFFRACTIONr_scangle_it2.8544.5765
X-RAY DIFFRACTIONr_rigid_bond_restr1.07432137
X-RAY DIFFRACTIONr_sphericity_free2.5433246
X-RAY DIFFRACTIONr_sphericity_bonded2.79431980
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 187 -
Rwork0.299 3538 -
obs--99.6 %

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