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- PDB-1te2: Putative Phosphatase Ynic from Escherichia coli K12 -

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Basic information

Entry
Database: PDB / ID: 1te2
TitlePutative Phosphatase Ynic from Escherichia coli K12
Components2-deoxyglucose-6-P phosphatase
KeywordsHYDROLASE / Structural Genomics / Phosphatase / Phosphates / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


mannitol-1-phosphatase / sorbitol-6-phosphatase / 2-deoxyglucose-6-phosphatase / 2-deoxyglucose-6-phosphatase activity / mannitol-1-phosphatase activity / glucose-6-phosphatase activity / sorbitol-6-phosphatase activity / sugar-phosphatase / sugar-phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases ...mannitol-1-phosphatase / sorbitol-6-phosphatase / 2-deoxyglucose-6-phosphatase / 2-deoxyglucose-6-phosphatase activity / mannitol-1-phosphatase activity / glucose-6-phosphatase activity / sorbitol-6-phosphatase activity / sugar-phosphatase / sugar-phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / carbohydrate metabolic process / magnesium ion binding / metal ion binding / cytosol
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-PHOSPHOGLYCOLIC ACID / 2-deoxyglucose-6-P phosphatase / Hexitol phosphatase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsKim, Y. / Joachimiak, A. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Phosphatase Ynic from Escherichia coli K12
Authors: Kim, Y. / Joachimiak, A. / Evdokimova, E. / Savchenko, A. / Edwards, A.
History
DepositionMay 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 17, 2015Group: Database references / Source and taxonomy / Structure summary
Revision 1.4Jun 24, 2015Group: Source and taxonomy
Remark 600HETEROGEN AUTHOR STATED THAT THE MISSING ATOMS OF 2PL MAY BE DUE TO DISORDER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-deoxyglucose-6-P phosphatase
B: 2-deoxyglucose-6-P phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6108
Polymers50,1372
Non-polymers4726
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-56 kcal/mol
Surface area17890 Å2
MethodPISA
2
B: 2-deoxyglucose-6-P phosphatase
hetero molecules

A: 2-deoxyglucose-6-P phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6108
Polymers50,1372
Non-polymers4726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area1810 Å2
ΔGint-55 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.591, 88.447, 48.591
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number4
Space group name H-MP1211
Detailsunknown, but most likely a dimer as it is in the asymmetric unit.

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Components

#1: Protein 2-deoxyglucose-6-P phosphatase


Mass: 25068.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3T7L2, UniProt: P77247*PLUS, phosphoglycolate phosphatase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O6P
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Fragment: 2-HYDROXY ETHYL PHOSPHATE / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Calcium Chloride PEG 3350 or PEGMME 3350, Sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9795, 0.956
DetectorType: SBC-2 / Detector: CCD / Date: Feb 18, 2004 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
30.9561
ReflectionResolution: 1.76→25.16 Å / Num. all: 39931 / Num. obs: 38493 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.9
Reflection shellResolution: 1.76→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.95 / Num. unique all: 2843 / % possible all: 71.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→25.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.238 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21964 3770 10 %RANDOM
Rwork0.17416 ---
all0.1787 39931 --
obs0.1787 33858 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-2.54 Å2
2---2.14 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.76→25.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 20 637 4007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223495
X-RAY DIFFRACTIONr_bond_other_d0.0020.023351
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9974760
X-RAY DIFFRACTIONr_angle_other_deg0.83437778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8025449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02524.126143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79715616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9161530
X-RAY DIFFRACTIONr_chiral_restr0.0670.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023873
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02643
X-RAY DIFFRACTIONr_nbd_refined0.3360.2973
X-RAY DIFFRACTIONr_nbd_other0.2580.24327
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.21988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2454
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1760.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7871.52326
X-RAY DIFFRACTIONr_mcbond_other0.1521.5884
X-RAY DIFFRACTIONr_mcangle_it1.1323615
X-RAY DIFFRACTIONr_scbond_it1.86331341
X-RAY DIFFRACTIONr_scangle_it2.8184.51145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.809 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 182 -
Rwork0.242 1617 -
obs-1617 0.72 %

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