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- PDB-2ipl: Crystal structure of a disulfide mutant glucose binding protein -

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Basic information

Entry
Database: PDB / ID: 2ipl
TitleCrystal structure of a disulfide mutant glucose binding protein
ComponentsD-galactose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / glucose binding protein / periplasmic binding protein / disulfide
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: 1.2 Å
AuthorsCuneo, M.J. / Hellinga, H.W.
CitationJournal: To be Published
Title: The free energy cost of domain reorganization in E. coli glucose binding protein
Authors: Cuneo, M.J. / Hellinga, H.W.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 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 1.5Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,7843
Polymers34,5641
Non-polymers2202
Water7,909439
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.840, 36.680, 79.070
Angle α, β, γ (deg.)90.00, 124.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34563.941 Da / Num. of mol.: 1 / Mutation: P70C, G151C
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 (bacteria) / Strain (production host): BL21 / References: UniProt: P0AEE5
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-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


Mass: 18.015 Da / Num. of mol.: 439 / 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: 40.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, pH7.5, 20% PEG 1500, 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: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 81424 / Num. obs: 81424 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.267 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.17
Reflection shellResolution: 1.2→1.3 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 3.7 / Num. measured obs: 35253 / Num. unique all: 13552 / % possible all: 72

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345data collection
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HPH

2hph


Resolution: 1.2→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.329 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4070 5 %RANDOM
Rwork0.167 ---
all0.168 81403 --
obs0.168 81403 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: 11.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.31 Å2
2--0.97 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 13 439 2990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222614
X-RAY DIFFRACTIONr_bond_other_d0.0010.021702
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.963584
X-RAY DIFFRACTIONr_angle_other_deg0.8793.0014235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4545359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23827.119118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56815465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.987157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023073
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02464
X-RAY DIFFRACTIONr_nbd_refined0.2180.2613
X-RAY DIFFRACTIONr_nbd_other0.1760.21874
X-RAY DIFFRACTIONr_nbtor_refined0.170.21357
X-RAY DIFFRACTIONr_nbtor_other0.0830.21308
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2331
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1470.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.233
X-RAY DIFFRACTIONr_mcbond_it0.8971.51733
X-RAY DIFFRACTIONr_mcbond_other0.3791.5675
X-RAY DIFFRACTIONr_mcangle_it1.322720
X-RAY DIFFRACTIONr_scbond_it1.83131009
X-RAY DIFFRACTIONr_scangle_it2.6164.5861
X-RAY DIFFRACTIONr_rigid_bond_restr0.94834706
X-RAY DIFFRACTIONr_sphericity_free3.6313444
X-RAY DIFFRACTIONr_sphericity_bonded2.1934253
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 190 -
Rwork0.243 3619 -
obs-3809 100 %

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