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- PDB-1urp: D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1urp
TitleD-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI
ComponentsD-RIBOSE-BINDING PROTEIN
KeywordsTRANSPORT / CHEMOTAXIS / PERIPLASM
Function / homology
Function and homology information


D-ribose transmembrane transport / monosaccharide binding / positive chemotaxis / 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
Ribose import binding protein RbsB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBjorkman, A.J. / Mowbray, S.L.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Multiple open forms of ribose-binding protein trace the path of its conformational change.
Authors: Bjorkman, A.J. / Mowbray, S.L.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Identical Mutations at Corresponding Positions in Two Homologous Proteins with Nonidentical Effects
Authors: Bjorkman, A.J. / Binnie, R.A. / Cole, L.B. / Zhang, H. / Hermodson, M.A. / Mowbray, S.L.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Probing Protein-Protein Interactions. The Ribose-Binding Protein in Bacterial Transport and Chemotaxis
Authors: Bjorkman, A.J. / Binnie, R.A. / Zhang, H. / Cole, L.B. / Hermodson, M.A. / Mowbray, S.L.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: 1.7 A X-Ray Structure of the Periplasmic Ribose Receptor from Escherichia Coli
Authors: Mowbray, S.L. / Cole, L.B.
#4: Journal: Protein Sci. / Year: 1992
Title: Functional Mapping of the Surface of Escherichia Coli Ribose-Binding Protein: Mutations that Affect Chemotaxis and Transport
Authors: Binnie, R.A. / Zhang, H. / Mowbray, S. / Hermodson, M.A.
History
DepositionApr 3, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-RIBOSE-BINDING PROTEIN
B: D-RIBOSE-BINDING PROTEIN
C: D-RIBOSE-BINDING PROTEIN
D: D-RIBOSE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)114,0304
Polymers114,0304
Non-polymers00
Water4,071226
1
A: D-RIBOSE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5071
Polymers28,5071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-RIBOSE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5071
Polymers28,5071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-RIBOSE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5071
Polymers28,5071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-RIBOSE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5071
Polymers28,5071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.099, 120.954, 64.131
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9989, -0.03879, -0.02574), (-0.04294, 0.9813, 0.1878), (0.01797, 0.1887, -0.9819)97.39, 4.166, 54.82
2given(-0.999775, 0.016085, 0.013852), (-0.018614, -0.977991, -0.207815), (0.010204, -0.208026, 0.97807)65.3835, 41.6507, 3.5743
3given(0.999941, -0.000271, -0.010897), (-0.000256, -0.999999, 0.001353), (-0.010897, -0.001351, -0.99994)29.9885, 28.2094, 58.6718
4given(-0.999858, -0.005052, -0.01609), (-0.007839, 0.983964, 0.178194), (0.014931, 0.178295, -0.983864)96.6949, 1.5694, 55.244
5given(-0.999934, 0.004817, 0.010458), (-0.006725, -0.981577, -0.19095), (0.009345, -0.191008, 0.981544)65.8155, 40.1201, 3.4293
6given(0.999991, 0.004003, 0.001231), (0.003987, -0.999918, 0.012153), (0.001279, -0.012147, -0.999925)30.0788, 28.1456, 58.7429
7given(-0.999328, -0.03636, -0.004615), (-0.036594, 0.982745, 0.181311), (-0.002057, 0.181358, -0.983415)97.4502, 3.586, 56.4375
8given(-0.999873, 0.015504, 0.003817), (-0.015951, -0.980683, -0.194952), (0.000721, -0.194989, 0.980805)66.007, 40.656, 3.8003
9given(0.999997, 0.002183, -0.000849), (0.002183, -0.999997, 0.000625), (-0.000848, -0.000627, -0.999999)30.052, 28.1827, 58.7408
10given(-0.999513, -0.025815, -0.01754), (-0.028429, 0.984961, 0.170423), (0.012877, 0.170838, -0.985215)97.3122, 3.1863, 55.6545
11given(-0.999909, 0.012881, 0.004043), (-0.013429, -0.979822, -0.199419), (0.001392, -0.199456, 0.979906)66.0376, 40.7513, 3.7883
12given(0.999964, 0.002286, 0.008186), (0.002091, -0.999714, 0.02382), (0.008238, -0.023802, -0.999683)29.9735, 27.9764, 58.6697

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Components

#1: Protein
D-RIBOSE-BINDING PROTEIN


Mass: 28507.424 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Cellular location: PERIPLASM / Plasmid: PCMB1 / Cellular location (production host): PERIPLASM / Gene (production host): RBSB / Production host: Escherichia coli (E. coli) / Strain (production host): MRI7 / References: UniProt: P02925
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
Description: RESOLUTION LIMITS 8-4 ANGSTROMS IN THE SEARCHES.
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: CRYSTALS WERE OBTAINED FROM SOLUTIONS OF 7.5 - 15 MG/ML RBP, 21% PEG4000, 50-100 MM SODIUM CITRATE, PH 4, 5% GLYCEROL, BY HANGING DROP VAPOUR DIFFUSION., pH 5.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5-15 mg/mlprotein1drop
221 %PEG40001reservoir
350-100 mMsodium citrate1reservoir
45 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9123
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9123 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 36827 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 4.6 / % possible all: 79.1
Reflection shell
*PLUS
% possible obs: 79.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY FOR LIGAND-FREE MUTANT RBP, MOLECULE B.

Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1905 5 %RANDOM
Rwork0.235 ---
obs-36827 90.7 %-
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8008 0 0 226 8234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_deg1.6
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg24
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.65

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