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- PDB-1xvi: Crystal Structure of YedP, phosphatase-like domain protein from E... -

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Basic information

Entry
Database: PDB / ID: 1xvi
TitleCrystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12
ComponentsPutative mannosyl-3-phosphoglycerate phosphatase
KeywordsHYDROLASE / hypothetical protein / conserved protein / phophatase-like domain / predicted hydrolase / Sucrose-6F-phosphate phosphohydrolase (S6PP) / structural genomics / protein structure initiative / PSI / MCSG / midwest center for structural genomics
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase activity / mannosylglycerate biosynthetic process / phosphatase activity / magnesium ion binding / cytosol
Similarity search - Function
Mannosyl-3-phosphoglycerate phosphatase / Putative mannosyl-3-phosphoglycerate phosphatase; domain 2 / HAD-superfamily hydrolase, superfamily IIB, MPGP / Threonyl-tRNA Synthetase; Chain A, domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Mannosyl-3-phosphoglycerate phosphatase / Putative mannosyl-3-phosphoglycerate phosphatase; domain 2 / HAD-superfamily hydrolase, superfamily IIB, MPGP / Threonyl-tRNA Synthetase; Chain A, domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsKim, Y. / Joachimiak, A. / Cymborowski, M. / Skarina, T. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12
Authors: Kim, Y. / Joachimiak, A. / Cymborowski, M. / Skarina, T. / Savchenko, A. / Edwards, A.
History
DepositionOct 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.
Remark 600HETEROGEN AUTHORS STATE THAT 1PE, PG4 and PGE are from PEG 4000.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative mannosyl-3-phosphoglycerate phosphatase
B: Putative mannosyl-3-phosphoglycerate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4908
Polymers61,6192
Non-polymers8716
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.783, 79.975, 75.471
Angle α, β, γ (deg.)90.00, 99.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative mannosyl-3-phosphoglycerate phosphatase / MPGP / YEDP


Mass: 30809.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: k12 / Gene: yedP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P76329, mannosyl-3-phosphoglycerate phosphatase

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Non-polymers , 5 types, 394 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.7 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.98016
SYNCHROTRONAPS 19-BM20.98032
Detector
TypeIDDetectorDateDetails
SBC-31CCDMay 30, 2004mirrors
SBC-32CCDMay 30, 2004mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.980161
20.980321
ReflectionResolution: 2.26→74.33 Å / Num. all: 30945 / Num. obs: 30085 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7
Reflection shellResolution: 2.26→2.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2868 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→74.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.553 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24334 2964 10.1 %RANDOM
Rwork0.18388 ---
all0.19 26247 --
obs0.19 26247 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.188 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-1.26 Å2
2---0.08 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.26→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 54 388 4166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9655267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60424.972181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1415647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6071521
X-RAY DIFFRACTIONr_chiral_restr0.0930.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022916
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21725
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9131.52414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59323801
X-RAY DIFFRACTIONr_scbond_it1.86431651
X-RAY DIFFRACTIONr_scangle_it2.954.51452
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.25 184
Rwork0.191 1736
obs-1736

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