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- PDB-1fhf: THE STRUCTURE OF SOYBEAN PEROXIDASE -

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Basic information

Entry
Database: PDB / ID: 1fhf
TitleTHE STRUCTURE OF SOYBEAN PEROXIDASE
ComponentsSEED COAT PEROXIDASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


peroxidase / lactoperoxidase activity / 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 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Plant peroxidase / Secretory peroxidase / 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 / Peroxidase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsHenriksen, A. / Mirza, O. / Indiana, C. / Welinder, K. / Teilum, K. / Gajhede, M.
CitationJournal: Protein Sci. / Year: 2001
Title: Structure of soybean seed coat peroxidase: a plant peroxidase with unusual stability and haem-apoprotein interactions.
Authors: Henriksen, A. / Mirza, O. / Indiani, C. / Teilum, K. / Smulevich, G. / Welinder, K.G. / Gajhede, M.
History
DepositionAug 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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: SEED COAT PEROXIDASE
B: SEED COAT PEROXIDASE
C: SEED COAT PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,23718
Polymers99,4143
Non-polymers2,82315
Water21612
1
A: SEED COAT PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0796
Polymers33,1381
Non-polymers9415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SEED COAT PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0796
Polymers33,1381
Non-polymers9415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SEED COAT PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0796
Polymers33,1381
Non-polymers9415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.454, 106.454, 104.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein SEED COAT PEROXIDASE


Mass: 33137.961 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Production host: Escherichia coli (E. coli) / References: UniProt: O22443, peroxidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M tris hcl, 0.6M ammoniumdihydrogenphosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
21.9 mg/mlprotein1drop
30.2-0.6 M1reservoirNH4H2PO4
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 24, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 2.8→11 Å / Num. all: 31053 / Num. obs: 26929 / % possible obs: 88.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.289 / Num. unique all: 1075 / % possible all: 69.3
Reflection
*PLUS
Lowest resolution: 11 Å / Num. measured all: 175095
Reflection shell
*PLUS
% possible obs: 69.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.8→11 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 356711.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1295 4.9 %RANDOM
Rwork0.271 ---
obs0.271 26625 87.2 %-
all-26625 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.7737 Å2 / ksol: 0.412803 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.81 Å27.05 Å20 Å2
2--3.81 Å20 Å2
3----7.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.8→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 0 183 12 7182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.111
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it2.182.5
Refine LS restraints NCSNCS model details: STRICT
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 133 5.3 %
Rwork0.376 2365 -
obs--46.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION3SOYBEAN_PARAM_cns.hemeWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5TRIS_CNS.PARTRIS_CNS.PAR
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.111
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.387 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.376

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