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- PDB-1nt4: Crystal structure of Escherichia coli periplasmic glucose-1-phosp... -

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Basic information

Entry
Database: PDB / ID: 1nt4
TitleCrystal structure of Escherichia coli periplasmic glucose-1-phosphatase H18A mutant complexed with glucose-1-phosphate
ComponentsGlucose-1-phosphatase
KeywordsHYDROLASE / alpha domain / alpha-beta domain / occluded active site / enzyme-substrate complex / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


glucose-1-phosphatase / glucose-1-phosphatase activity / 3-phytase activity / sugar-phosphatase activity / glucose catabolic process / dephosphorylation / outer membrane-bounded periplasmic space
Similarity search - Function
Histidine acid phosphatases active site signature. / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-O-phosphono-beta-D-glucopyranose / Glucose-1-phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsLee, D.C. / Cottrill, M.A. / Forsberg, C.W. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Functional insights revealed by the crystal structures of Escherichia coli glucose-1-phosphatase.
Authors: Lee, D.C. / Cottrill, M.A. / Forsberg, C.W. / Jia, Z.
History
DepositionJan 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Aug 18, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_chem_comp_identifier.comp_id / _pdbx_chem_comp_identifier.identifier / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2
Revision 2.1Oct 27, 2021Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-1-phosphatase
B: Glucose-1-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5954
Polymers87,0742
Non-polymers5202
Water6,323351
1
A: Glucose-1-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7972
Polymers43,5371
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-1-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7972
Polymers43,5371
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.263, 156.263, 84.575
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Glucose-1-phosphatase / G1Pase


Mass: 43537.117 Da / Num. of mol.: 2 / Mutation: H18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AGP OR B1002 / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): SBS1572 / References: UniProt: P19926, glucose-1-phosphatase
#2: Sugar ChemComp-XGP / 1-O-phosphono-beta-D-glucopyranose / 1-O-phosphono-beta-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, PEG 500 mme, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.25 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
21.75-1.2 Mammonium sulfate1reservoir
325 %(w/v)PEG5000 MME1reservoir
40.05 MMES1reservoirpH6.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.2146, 1.2149, 1.3190
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21461
21.21491
31.3191
ReflectionResolution: 2.4→30 Å / Num. all: 27106 / Num. obs: 27106 / % possible obs: 91.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.45 % / Rsym value: 0.078 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 3023 / Rsym value: 0.271 / % possible all: 91.1
Reflection
*PLUS
Num. obs: 27760 / Num. measured all: 95761 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 91.1 % / Rmerge(I) obs: 0.271

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1388 -random
Rwork0.218 ---
all0.228 27760 --
obs0.218 26181 91.9 %-
Displacement parametersBiso mean: 29.75 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 32 351 6499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.42
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.284 1388 -
Rwork0.218 --
obs-27760 91.9 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.2179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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