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- PDB-1bgp: CRYSTAL STRUCTURE OF BARLEY GRAIN PEROXIDASE 1 -

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Basic information

Entry
Database: PDB / ID: 1bgp
TitleCRYSTAL STRUCTURE OF BARLEY GRAIN PEROXIDASE 1
ComponentsBARLEY GRAIN PEROXIDASE
KeywordsOXIDOREDUCTASE / PEROXIDASE / CHROMOPROTEIN
Function / homologyHaem peroxidase superfamily / Peroxidases heam-ligand binding site / Plant heme peroxidase family profile. / Peroxidases active site signature. / Peroxidases proximal heme-ligand signature. / Peroxidase / Secretory peroxidase / Plant peroxidase / Haem peroxidase / Peroxidase, active site ...Haem peroxidase superfamily / Peroxidases heam-ligand binding site / Plant heme peroxidase family profile. / Peroxidases active site signature. / Peroxidases proximal heme-ligand signature. / Peroxidase / Secretory peroxidase / Plant peroxidase / Haem peroxidase / Peroxidase, active site / peroxidase / peroxidase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding / Peroxidase
Function and homology information
Specimen sourceHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.9 Å resolution
AuthorsHenriksen, A.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Structure of barley grain peroxidase refined at 1.9-A resolution. A plant peroxidase reversibly inactivated at neutral pH.
Authors: Henriksen, A. / Welinder, K.G. / Gajhede, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 24, 1997 / Release: Nov 12, 1997
RevisionDateData content typeGroupProviderType
1.0Nov 12, 1997Structure modelrepositoryInitial release
1.1Mar 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BARLEY GRAIN PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5454
Polyers33,8651
Non-polymers6803
Water2,630146
1
A: BARLEY GRAIN PEROXIDASE
hetero molecules

A: BARLEY GRAIN PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0898
Polyers67,7302
Non-polymers1,3596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
γ
α
β
Length a, b, c (Å)71.920, 105.060, 40.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide BARLEY GRAIN PEROXIDASE


Mass: 33865.188 Da / Num. of mol.: 1 / Source: (natural) Hordeum vulgare (barley) / Genus: Hordeum / References: UniProt: Q40069, peroxidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Formula: C34H32FeN4O4 / Heme
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Formula: H2O / Water

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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: 2.28 / Density percent sol: 46.12 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Henriksen, A., (1992) J. Mol. Biol., 228, 690.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
110 mg/mlprotein1drop
220 %PEG60001reservoir
30.01 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 287 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Details: COLLIMATOR / Detector: IMAGE PLATE / Collection date: Mar 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 18.9 Å2 / D resolution high: 1.9 Å / D resolution low: 38 Å / Number obs: 24371 / Observed criterion sigma I: 0 / Rmerge I obs: 0.097 / Rsym value: 0.088 / NetI over sigmaI: 7.4 / Redundancy: 5.8 % / Percent possible obs: 96.8
Reflection shellHighest resolution: 1.9 Å / Lowest resolution: 1.99 Å / MeanI over sigI obs: 1.8 / Rsym value: 0.416 / Redundancy: 3.7 % / Percent possible all: 81.4
Reflection
*PLUS
Number measured all: 140862 / Rmerge I obs: 0.088
Reflection shell
*PLUS
Percent possible obs: 81.4 / Rmerge I obs: 0.416

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SCH, POLY-ALA CHAIN
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Sigma F: 0
Displacement parametersB iso mean: 23.5 Å2
Least-squares processR factor R free: 0.23 / R factor R work: 0.192 / R factor obs: 0.192 / Highest resolution: 1.9 Å / Lowest resolution: 38 Å / Number reflection obs: 24371 / Percent reflection R free: 1 / Percent reflection obs: 96.8
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 3 Å / Luzzati sigma a obs: 0.23 Å
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 38 Å
Number of atoms included #LASTProtein: 2934 / Nucleic acid: 0 / Ligand: 45 / Solvent: 146 / Total: 3125
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.821.50
X-RAY DIFFRACTIONx_mcangle_it2.802.00
X-RAY DIFFRACTIONx_scbond_it3.352.00
X-RAY DIFFRACTIONx_scangle_it5.072.50
Refine LS shellHighest resolution: 1.9 Å / R factor R work: 0.298 / Lowest resolution: 1.99 Å / Number reflection R work: 2457 / Total number of bins used: 8 / Percent reflection obs: 81.4
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.HEMETOPH.HEME
X-RAY DIFFRACTION3PARAM.CATTOPH.CAT
X-RAY DIFFRACTION4PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.23
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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