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- PDB-1qdm: CRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR... -

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Basic information

Entry
Database: PDB / ID: 1qdm
TitleCRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR ASPARTIC PROTEINASE.
ComponentsPROPHYTEPSIN
KeywordsHYDROLASE / ASPARTIC PROTEINASES / PHYTEPSIN / SAPOSIN-LIKE DOMAIN / ZYMOGEN STRUCTURE
Function / homology
Function and homology information


phytepsin / vacuole / lipid metabolic process / aspartic-type endopeptidase activity
Similarity search - Function
Phytepsin / Saposin-like / NK-Lysin / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like ...Phytepsin / Saposin-like / NK-Lysin / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsKervinen, J. / Tobin, G.J. / Costa, J. / Waugh, D.S. / Wlodawer, A. / Zdanov, A.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting.
Authors: Kervinen, J. / Tobin, G.J. / Costa, J. / Waugh, D.S. / Wlodawer, A. / Zdanov, A.
History
DepositionMay 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROPHYTEPSIN
B: PROPHYTEPSIN
C: PROPHYTEPSIN


Theoretical massNumber of molelcules
Total (without water)153,9853
Polymers153,9853
Non-polymers00
Water00
1
A: PROPHYTEPSIN


Theoretical massNumber of molelcules
Total (without water)51,3281
Polymers51,3281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROPHYTEPSIN


Theoretical massNumber of molelcules
Total (without water)51,3281
Polymers51,3281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROPHYTEPSIN


Theoretical massNumber of molelcules
Total (without water)51,3281
Polymers51,3281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.0, 160.9, 81.4
Angle α, β, γ (deg.)90.0, 109.6, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe monomer is biologically active molecule.

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Components

#1: Protein PROPHYTEPSIN


Mass: 51328.402 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / References: UniProt: P42210, phytepsin

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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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 15% PEG 6000, 50mM MAGNESIUM ACETATE, 0.1M SODIUM CACODYLATE, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMTris-HCl1drop
30.1 M1dropNaCl
415 %PEG60001reservoir
550 mMmagnesium acetate1reservoir
60.1 Msodium cacodylate1reservoir
70.02 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. all: 70907 / Num. obs: 49301 / % possible obs: 69.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.25 / Num. unique all: 1059 / % possible all: 29.6
Reflection shell
*PLUS
% possible obs: 29.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4& PHASESmodel building
X-PLORrefinement
CCP4phasing
PHASESphasing
RefinementResolution: 2.3→10 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.224 --
all0.224 49301 -
obs0.224 42242 60.3 %
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9336 0 0 0 9336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.8
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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