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- PDB-2b0c: The crystal structure of the putative phosphatase from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 2b0c
TitleThe crystal structure of the putative phosphatase from Escherichia coli
Componentsputative phosphatase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / phosphatase / alpha-d-glucose-1-phosphate / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


glucose-1-phosphatase / glucose-1-phosphatase activity / manganese ion binding / magnesium ion binding
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / 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
1-O-phosphono-alpha-D-glucopyranose / Alpha-D-glucose 1-phosphate phosphatase YihX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 2.0A crystal structure of the putative phosphatase from Escherichia coli
Authors: Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionSep 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8613
Polymers23,5771
Non-polymers2842
Water2,900161
1
A: putative phosphatase
hetero molecules

A: putative phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7226
Polymers47,1542
Non-polymers5694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)62.256, 62.256, 127.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThis protein may existed as dimer. The second part of the dimer is generated by the operation: 1/2-x,1/2+y,1/4-z

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Components

#1: Protein putative phosphatase /


Mass: 23576.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yihX / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A8Y3
#2: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.61 Å3/Da / Density % sol: 52 % / Description: Freidel pairs were used.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.05M MES, 25% PEG 5KMME, 0.2M (NH4)2SO4, 10mM MgCl2, pH 5.6, 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: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 32264 / Num. obs: 32006 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 56.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.35 / Num. unique all: 3234 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.309 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 885 5.1 %RANDOM
Rwork0.20058 ---
all0.207 16697 --
obs0.20337 16597 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.071 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 17 161 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211662
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9452255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7692485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20915272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2871510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021272
X-RAY DIFFRACTIONr_nbd_refined0.2120.2788
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2147
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.213
X-RAY DIFFRACTIONr_mcbond_it0.7661.51034
X-RAY DIFFRACTIONr_mcangle_it1.29721600
X-RAY DIFFRACTIONr_scbond_it2.223726
X-RAY DIFFRACTIONr_scangle_it3.3934.5655
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 58 -
Rwork0.261 1130 -
obs--94.74 %

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