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- PDB-7e7m: Crystal Structure Analysis of the Streptococcus agalactiae Ribose... -

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Basic information

Entry
Database: PDB / ID: 7e7m
TitleCrystal Structure Analysis of the Streptococcus agalactiae Ribose Binding Protein RbsB
ComponentsD-ribose ABC transporter substrate-binding protein
KeywordsSUGAR BINDING PROTEIN / Protein-ribose complex
Function / homologybeta-D-ribopyranose / :
Function and homology information
Biological speciesStreptococcus agalactiae ZQ0910 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPan, L.X. / Wang, B. / Yang, L.Y. / Yang, D.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31860245 China
National Natural Science Foundation of China (NSFC)31702386 China
CitationJournal: To be published
Title: Crystal Structure Analysis of the Streptococcus agalactiae Ribose Binding Protein RbsB
Authors: Pan, L.X. / Wang, B. / Yang, L.Y. / Yang, D.F.
History
DepositionFeb 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: D-ribose ABC transporter substrate-binding protein
B: D-ribose ABC transporter substrate-binding protein
C: D-ribose ABC transporter substrate-binding protein
D: D-ribose ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,0978
Polymers136,4974
Non-polymers6014
Water1448
1
A: D-ribose ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2742
Polymers34,1241
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-ribose ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2742
Polymers34,1241
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-ribose ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2742
Polymers34,1241
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-ribose ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2742
Polymers34,1241
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.631, 151.220, 169.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
D-ribose ABC transporter substrate-binding protein / D-ribose transporter subunit RbsB / Ribose ABC transporter / periplasmic D-ribose-binding protein


Mass: 34124.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae ZQ0910 (bacteria)
Gene: rbsB / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6H3FYP2
#2: Sugar
ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.86 Å3/Da / Density % sol: 34.03 % / Description: plate
Crystal growTemperature: 293 K / Method: evaporation / pH: 7 / Details: jeffamime ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.85→39.63 Å / Num. obs: 22672 / % possible obs: 94.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 54.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.055 / Rrim(I) all: 0.134 / Net I/σ(I): 11.7 / Num. measured all: 121350 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.85-35.30.65233750.7580.3010.72297.2
9.01-39.635.60.0286740.9990.0120.0384.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IOY

2ioy


Resolution: 2.85→38.59 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1139 5.03 %
Rwork0.2102 21507 -
obs0.2126 22646 91.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.51 Å2 / Biso mean: 57.5412 Å2 / Biso min: 26.03 Å2
Refinement stepCycle: final / Resolution: 2.85→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8313 0 40 8 8361
Biso mean--46.85 39.24 -
Num. residues----1120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.980.34131480.30152717286595
2.98-3.140.32761340.27212740287495
3.14-3.330.32831460.26732765291194
3.33-3.590.32211520.24082707285993
3.59-3.950.25861290.21012695282492
3.95-4.520.24041280.18342646277490
4.52-5.690.21141600.18642645280588
5.7-38.590.20891420.16522592273483

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