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- PDB-1rpj: CRYSTAL STRUCTURE OF D-ALLOSE BINDING PROTEIN FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1rpj
TitleCRYSTAL STRUCTURE OF D-ALLOSE BINDING PROTEIN FROM ESCHERICHIA COLI
ComponentsPROTEIN (PRECURSOR OF PERIPLASMIC SUGAR RECEPTOR)
KeywordsPERIPLASMIC SUGAR RECEPTOR
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
beta-D-allopyranose / D-allose-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChaudhuri, B. / 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
DepositionFeb 4, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2017Group: Atomic model / Category: atom_site
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.label_atom_id
Revision 2.1Jul 29, 2020Group: Data collection / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PRECURSOR OF PERIPLASMIC SUGAR RECEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7594
Polymers30,4181
Non-polymers3423
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.380, 67.820, 53.590
Angle α, β, γ (deg.)90.00, 96.71, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein PROTEIN (PRECURSOR OF PERIPLASMIC SUGAR RECEPTOR) / ALBP


Mass: 30417.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / Cellular location: PERIPLASM / Species: Escherichia coli / Strain: K-12 / References: UniProt: P39265
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-ALL / beta-D-allopyranose / beta-D-allose / D-allose / allose / D-ALLOPYRANOSE


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DAllpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-allopyranoseCOMMON NAMEGMML 1.0
b-D-AllpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AllSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsZINC SULFATE WAS ESSENTIAL FOR CRYSTALLIZATION AND BOTH ZINC AND SULFATE IONS COULD BE MODELLED IN ...ZINC SULFATE WAS ESSENTIAL FOR CRYSTALLIZATION AND BOTH ZINC AND SULFATE IONS COULD BE MODELLED IN THE DENSITY. THE ZINC ION IS OBSERVED IN OCTAHEDRAL COORDINATION WOTH BOTH AMINO AND CARBONYL GROUPS OF THE N-TERMINAL RESIDUE AND FOUR WATER MOLECULES. THESE WATER MOLECULES MEDIATE INTERACTIONS WITH THE SIDE CHAINS OF A SYMMETRY RELATED MOLECULE.

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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: 1.98 Å3/Da / Density % sol: 41 %
Crystal growpH: 6.5 / Details: pH 6.5
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 55011
2ZnSO411
3MES BUFFER11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMHEPES1drop
340-60 %(v/v)mPEG5501reservoir
40.01 Mzinc sulfate1reservoir
50.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.787 Å / Num. obs: 21163 / % possible obs: 96.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 17.07 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5 / % possible all: 93.6
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DRI

2dri


Resolution: 1.8→29 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: CNS WAS USED BEFORE REFMAC FOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1295 6.1 %RANDOM
Rwork0.194 ---
all-22055 --
obs-22055 96.5 %-
Displacement parametersBiso mean: 11.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 18 215 2366
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0240.03
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1620.3
X-RAY DIFFRACTIONp_planar_tor4.27
X-RAY DIFFRACTIONp_staggered_tor15.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.620
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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