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- PDB-1xri: X-ray structure of a putative phosphoprotein phosphatase from Ara... -

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Basic information

Entry
Database: PDB / ID: 1xri
TitleX-ray structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene AT1G05000
ComponentsAt1g05000
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / PSI / CESG / Center for Eukaryotic Structural Genomics / AT1G05000 / phosphoprotein phosphatase
Function / homology
Function and homology information


phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Atypical dual-specificity phosphatase Siw14-like, plant and fungi / Atypical dual-specificity phosphatase Siw14-like / Tyrosine phosphatase family / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like ...Atypical dual-specificity phosphatase Siw14-like, plant and fungi / Atypical dual-specificity phosphatase Siw14-like / Tyrosine phosphatase family / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase DSP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, SAD / MAD / Resolution: 3.3 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2008
Title: Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000.
Authors: Aceti, D.J. / Bitto, E. / Yakunin, A.F. / Proudfoot, M. / Bingman, C.A. / Frederick, R.O. / Sreenath, H.K. / Vojtik, F.C. / Wrobel, R.L. / Fox, B.G. / Markley, J.L. / Phillips Jr., G.N.
History
DepositionOct 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 6, 2013Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: At1g05000
B: At1g05000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4646
Polymers35,0802
Non-polymers3844
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-82 kcal/mol
Surface area14590 Å2
MethodPISA
2
A: At1g05000
B: At1g05000
hetero molecules

A: At1g05000
B: At1g05000
hetero molecules

A: At1g05000
B: At1g05000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,39218
Polymers105,2406
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area13690 Å2
ΔGint-289 kcal/mol
Surface area37610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.483, 124.483, 124.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein At1g05000


Mass: 17539.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: pQE derivative / Gene: At1g05000 / Plasmid: pVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9ZVN4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 MG/ML PROTEIN 0.60 M AMMONIUM SULFATE, .100 M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 19-BM10.97930.9793
SYNCHROTRONAPS 14-ID-B20.9790.979
Detector
TypeIDDetectorDateDetails
APS-11CCDJul 31, 2004sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
MAR CCD 165 mm2CCDAug 8, 2004bent cylindrical Si-mirror (Rh coating)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal monochromator, water cooledMADMx-ray1
2Diamond (111) double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.9791
ReflectionResolution: 3.3→44.01 Å / Num. all: 18774 / Num. obs: 18774 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.6 % / Limit h max: 37 / Limit h min: 2 / Limit k max: 26 / Limit k min: 2 / Limit l max: 26 / Limit l min: -26 / Observed criterion F max: 147635.48 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.115 / Net I/σ(I): 20.8
Reflection shell

Mean I/σ(I) obs: 10.3 / Diffraction-ID: 1,2 / Redundancy: 22.2 %

Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
3.3-3.380.2916570.949100
3.38-3.460.246681.022100
3.46-3.550.196370.996100
3.55-3.660.1576660.976100
3.66-3.780.146661.083100
3.78-3.910.1326441.123100
3.91-4.070.1086511.118100
4.07-4.250.0976521.114100
4.25-4.480.0966661.032100
4.48-4.760.0846611.057100
4.76-5.130.0936711.103100
5.13-5.640.1156711.079100
5.64-6.460.1376741.047100
6.46-8.130.0956771.032100
8.13-500.0557281.12899.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MADD res high: 3.5 Å / D res low: 20 Å / FOM : 0.44 / Reflection: 8211
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1110.979514.06-11.01
1120.97939.56-2
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1118.2615.97131.96SE22.90.16
27.754124.50126.03SE600.32
3121.34133.78123.893SE600.25
41.9650.08325.229SE600.26
Phasing MAD shell
Resolution (Å)FOM Reflection
11.16-200.62480
7.54-11.160.61717
6.04-7.540.54874
5.18-6.040.511022
4.61-5.180.461137
4.19-4.610.421234
3.87-4.190.361311
3.61-3.870.291436
Phasing dmFOM : 0.74 / FOM acentric: 0.75 / FOM centric: 0.63 / Reflection: 9971 / Reflection acentric: 8874 / Reflection centric: 1097
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.4-44.0110.930.930.77470344126
5.9-9.40.780.810.6613511142209
4.7-5.90.780.810.6316751476199
4.1-4.70.80.820.6716661503163
3.5-4.10.740.750.6129752718257
3.3-3.50.560.570.4718341691143

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
CNS1.1refinement
PDB_EXTRACT1data extraction
RefinementMethod to determine structure: MAD, SAD / Resolution: 3.3→44.01 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.59 / Cross valid method: THROUGHOUT
Details: Selenium F' and F'' adjusted for wavelength. Molprobity used to assist in final model building. The Friedel pairs were used in phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1736 9.4 %RANDOM
Rwork0.204 ---
all-18774 --
obs-18486 98.5 %-
Solvent computationSolvent model: bulk solvent / Bsol: 39.628 Å2 / ksol: 0.343235 e/Å3
Displacement parametersBiso max: 157.13 Å2 / Biso mean: 29.12 Å2 / Biso min: 2.25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 3.3→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 20 60 2528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg21
X-RAY DIFFRACTIONx_torsion_impr_deg0.93
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.3-3.450.28523610.30.2220480.0192409228494.8
3.45-3.630.26223210.20.19320320.0172350226496.3
3.63-3.860.2322058.70.17921400.0162392234598
3.86-4.160.2151737.50.17621400.0162333231399.1
4.16-4.580.223510.10.16320820.0132337231799.1
4.58-5.240.193232100.15220990.0132347233199.3
5.24-6.60.35120790.26720820.0242325228998.5
6.6-44.010.3072169.20.29421270.0212359234399.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION20_cis_peptide.paramcarbohydrate.top
X-RAY DIFFRACTION3water.param
X-RAY DIFFRACTION4ion.param

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