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

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Basic information

Entry
Database: PDB / ID: 1gud
TitleHinge-bending motion of D-allose binding protein from Escherichia coli: three open conformations
ComponentsD-ALLOSE-BINDING PERIPLASMIC PROTEIN
KeywordsPERIPLASMIC 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 / transmembrane transport / 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
D-allose-binding periplasmic protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 1.3Dec 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.ptnr1_auth_asym_id / _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_asym_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_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
B: D-ALLOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,35910
Polymers60,8362
Non-polymers5238
Water8,953497
1
A: D-ALLOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6795
Polymers30,4181
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: D-ALLOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6795
Polymers30,4181
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.229, 64.096, 142.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


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


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.25 Å3/Da / Density % sol: 45.2 %
Crystal growpH: 8 / Details: pH 8.00
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
330 %PEG40001reservoir
40.1 MTris-HCl1reservoir
55 mM1reservoirZn2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94
DetectorDate: Dec 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.71→35.58 Å / Num. obs: 8404 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.0093 / Net I/σ(I): 13.9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.036 / Mean I/σ(I) obs: 6.3 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.362

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPJ

1rpj


Resolution: 1.71→70.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.875 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2341 3.9 %RANDOM
Rwork0.172 ---
obs0.173 58061 99.9 %-
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: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.71→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 8 497 4770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224331
X-RAY DIFFRACTIONr_bond_other_d0.0020.024032
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9665842
X-RAY DIFFRACTIONr_angle_other_deg0.81239430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3085574
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_restr0.0960.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
X-RAY DIFFRACTIONr_nbd_refined0.2150.2891
X-RAY DIFFRACTIONr_nbd_other0.2420.24449
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9371.52852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65624548
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.94831479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7184.51294
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: 1.71→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.218 161
Rwork0.188 4181
Refinement
*PLUS
Lowest resolution: 35.58 Å / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.025
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.1
LS refinement shell
*PLUS
Highest resolution: 1.71 Å / Lowest resolution: 1.76 Å / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.169

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