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- PDB-2hph: High resolution structure of E. coli glucose/galactose binding pr... -

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Basic information

Entry
Database: PDB / ID: 2hph
TitleHigh resolution structure of E. coli glucose/galactose binding protein bound with glucose
ComponentsD-galactose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / GBP / glucose binding protein / chemotaxis
Function / homology
Function and homology information


methylgalactoside transport / galactose transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chemotaxis / outer membrane-bounded periplasmic space / carbohydrate binding / calcium ion binding / membrane
Similarity search - Function
D-galactose-binding periplasmic protein MglB-like, PBP domain / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / D-galactose/methyl-galactoside binding periplasmic protein MglB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsCuneo, M.J. / Hellinga, H.W.
CitationJournal: To be Published
Title: High resolution structure of E. coli glucose/galactose binding protein bound with glucose
Authors: Cuneo, M.J. / Johnson, S.J. / Beese, L.S. / Hellinga, H.W.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-galactose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5883
Polymers34,3681
Non-polymers2202
Water9,422523
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.260, 36.580, 64.940
Angle α, β, γ (deg.)90.00, 107.19, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein D-galactose-binding periplasmic protein / GBP / D-galactose/D-glucose-binding protein / GGBP


Mass: 34367.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mglB / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P0AEE5
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG6000, 50mM NaHEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.33→25 Å / Num. all: 62566 / Num. obs: 62566 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.341 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 5.22
Reflection shellResolution: 1.33→1.5 Å / % possible obs: 89.2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.18 / Num. measured obs: 49507 / Num. unique all: 18133 / Num. unique obs: 17054 / % possible all: 94.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GBP

2gbp


Resolution: 1.33→24.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.557 / SU ML: 0.03 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3129 5 %RANDOM
Rwork0.154 ---
all0.155 62566 --
obs0.155 62564 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.717 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.12 Å2
2--0.44 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.33→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 13 523 2924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222449
X-RAY DIFFRACTIONr_bond_other_d0.0010.021613
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9633339
X-RAY DIFFRACTIONr_angle_other_deg0.88134012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4685331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85227.08113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54615442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.104156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_nbd_refined0.2250.2547
X-RAY DIFFRACTIONr_nbd_other0.180.21719
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21227
X-RAY DIFFRACTIONr_nbtor_other0.0850.21202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2346
X-RAY DIFFRACTIONr_metal_ion_refined0.080.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.257
X-RAY DIFFRACTIONr_mcbond_it1.0831.51616
X-RAY DIFFRACTIONr_mcbond_other0.3851.5634
X-RAY DIFFRACTIONr_mcangle_it1.43722500
X-RAY DIFFRACTIONr_scbond_it2.1853963
X-RAY DIFFRACTIONr_scangle_it3.0594.5825
X-RAY DIFFRACTIONr_rigid_bond_restr1.00134443
X-RAY DIFFRACTIONr_sphericity_free4.4823524
X-RAY DIFFRACTIONr_sphericity_bonded1.98434013
LS refinement shellResolution: 1.33→1.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 187 -
Rwork0.227 3544 -
obs-3731 100 %

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