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- PDB-3rfi: Crystal structure of the saposin-like domain of plant aspartic pr... -

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Basic information

Entry
Database: PDB / ID: 3rfi
TitleCrystal structure of the saposin-like domain of plant aspartic protease from Solanum tuberosum
ComponentsAsp
KeywordsHYDROLASE / Aspartic protease / PSI / Saposin
Function / homology
Function and homology information


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 type domain / Saposin-like / Saposin B type domain profile. ...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 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBhaumik, P. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Mechanism of the Saposin-like Domain of a Plant Aspartic Protease.
Authors: Bryksa, B.C. / Bhaumik, P. / Magracheva, E. / De Moura, D.C. / Kurylowicz, M. / Zdanov, A. / Dutcher, J.R. / Wlodawer, A. / Yada, R.Y.
History
DepositionApr 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Aug 24, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asp


Theoretical massNumber of molelcules
Total (without water)11,7801
Polymers11,7801
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Asp

A: Asp


Theoretical massNumber of molelcules
Total (without water)23,5592
Polymers23,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3490 Å2
ΔGint-43 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.470, 56.470, 55.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

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Components

#1: Protein Asp


Mass: 11779.507 Da / Num. of mol.: 1 / Fragment: StAP_PSI (UNP Residues 301-403)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3)pLysS / References: UniProt: Q6B9W9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate monohydrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 8363 / Num. obs: 8355 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.87 / Num. unique all: 1159 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.179 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 417 5 %RANDOM
Rwork0.18697 ---
obs0.18995 7936 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms620 0 0 63 683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022645
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.978873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.703580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.42327.30826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08415128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.286151
X-RAY DIFFRACTIONr_chiral_restr0.1460.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021460
X-RAY DIFFRACTIONr_mcbond_it1.0491.5401
X-RAY DIFFRACTIONr_mcangle_it1.9832653
X-RAY DIFFRACTIONr_scbond_it3.8073244
X-RAY DIFFRACTIONr_scangle_it6.2984.5219
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 30 -
Rwork0.342 573 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6669-2.33372.486.6758-0.51944.93680.0406-0.122-0.18840.04190.0140.15020.3919-0.0247-0.05460.1165-0.0414-0.02570.1940.0270.077921.53217.1377.673
22.36370.2094-0.54546.4362-4.89176.64840.0093-0.05190.21650.2657-0.0611-0.0592-0.54630.08290.05190.1224-0.0047-0.02880.1047-0.02840.07545.19632.676-2.875
313.2676-6.6944-3.62877.40461.59434.6212-0.1935-0.3067-0.72080.38810.13060.46530.4765-0.05160.06290.2093-0.02670.00350.12710.03510.165916.9029.2532.977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 26
2X-RAY DIFFRACTION2A27 - 82
3X-RAY DIFFRACTION3A83 - 103

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