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- PDB-1gub: Hinge-bending motion of D-allose binding protein from Escherichia... -

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Basic information

Entry
Database: PDB / ID: 1gub
TitleHinge-bending motion of D-allose binding protein from Escherichia coli: three open conformations
ComponentsD-ALLOSE-BINDING PERIPLASMIC PROTEIN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / ALLOSE / HINGE BENDING / CONFORMATIONAL CHANGE
Function / homology
Function and homology information


D-allose transmembrane transport / D-ribose transmembrane transport / monosaccharide binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
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
NICKEL (II) ION / D-allose-binding periplasmic protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMagnusson, U. / Chaudhuri, B.N. / Ko, J. / Park, C. / Jones, T.A. / Mowbray, S.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structure of D-Allose Binding Protein from Escherichia Coli Bound to D-Allose at 1.8 A Resolution
Authors: Chaudhuri, B.N. / Ko, J. / Park, C. / Jones, T.A. / Mowbray, S.L.
#1: Journal: J.Bacteriol. / Year: 1997
Title: The D-Allose Operon of Escherichia Coli K-12
Authors: Kim, C. / Song, S. / Park, C.
History
DepositionJan 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-ALLOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4772
Polymers30,4181
Non-polymers591
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.100, 133.100, 133.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

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Components

#1: Protein D-ALLOSE-BINDING PERIPLASMIC PROTEIN / ALBP


Mass: 30417.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K12 / References: UniProt: P39265
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.23 Å3/Da / Density % sol: 62 %
Crystal growpH: 9 / Details: pH 9.00
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
210 mMHEPES1droppH7.8
320-30 %PEG2000MME1reservoir
40.1 MTris-HCl1reservoirpH9.0
50.01 M1reservoirNiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.89
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.08→29 Å / Num. obs: 625 / % possible obs: 99.5 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.0094 / Net I/σ(I): 7.1
Reflection shellResolution: 3.08→3.16 Å / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 29 Å / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.338

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPJ
Resolution: 3.1→29.75 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.781 / SU B: 27.453 / SU ML: 0.503 / Cross valid method: THROUGHOUT / ESU R Free: 0.589 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.339 550 7.1 %RANDOM
Rwork0.28 ---
obs0.284 7191 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.37 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 1 10 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0740.0222161
X-RAY DIFFRACTIONr_bond_other_d0.0420.022016
X-RAY DIFFRACTIONr_angle_refined_deg3.291.9662921
X-RAY DIFFRACTIONr_angle_other_deg2.41434715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3580.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022422
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02377
X-RAY DIFFRACTIONr_nbd_refined0.2310.2482
X-RAY DIFFRACTIONr_nbd_other0.2310.22351
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1220.21476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.8860.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.6280.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.3671.51425
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.19122274
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3383736
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9414.5647
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 30
Rwork0.286 515
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 29 Å / Num. reflection obs: 7260 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.024
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.5
LS refinement shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.28 Å / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.259

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