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- PDB-1uqw: Crystal structure of yliB protein from escherichia coi -

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Basic information

Entry
Database: PDB / ID: 1uqw
TitleCrystal structure of yliB protein from escherichia coi
ComponentsPUTATIVE BINDING PROTEIN YLIB
KeywordsZN BINDING PROTEIN / TRANSPORT / LIPOPROTEIN / BACTERIAL TARGETS AT IGS-CNRS / FRANCE / BIGS / STRUCTURAL GENOMICS
Function / homology
Function and homology information


dipeptide transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / DNA damage response
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione-binding protein GsiB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.72 Å
AuthorsJeudy, S. / Abergel, C. / Claverie, J.M.
CitationJournal: To be Published
Title: Crystal Structure of Ylib Protein from E.Coli
Authors: Jeudy, S. / Abergel, C. / Claverie, J.M.
History
DepositionOct 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE BINDING PROTEIN YLIB
B: PUTATIVE BINDING PROTEIN YLIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,09316
Polymers114,1242
Non-polymers96914
Water5,567309
1
A: PUTATIVE BINDING PROTEIN YLIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,90013
Polymers57,0621
Non-polymers83812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PUTATIVE BINDING PROTEIN YLIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1933
Polymers57,0621
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)152.560, 82.540, 93.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2144-

HOH

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Components

#1: Protein PUTATIVE BINDING PROTEIN YLIB


Mass: 57061.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P75797
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPEPTIDE SIGNAL CORRESPONDING TO THE 23 FIRST RESIDUES HAS BEEN REMOVED AND REPLACED WITH THE 22 ...PEPTIDE SIGNAL CORRESPONDING TO THE 23 FIRST RESIDUES HAS BEEN REMOVED AND REPLACED WITH THE 22 RESIDUES OF GATEWAY SEQUENCE TAG

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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: 2.58 Å3/Da / Density % sol: 52 %
Crystal growpH: 6
Details: PEG 8000 15%, ZINC ACETATE 0.2M, SODIUM ACETATE 0.1M PH6.0, GLYCEROL 5%, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98025,0.98051,0.96
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2002 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980251
20.980511
30.961
ReflectionResolution: 2.7→32.4 Å / Num. obs: 32994 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.2
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.72→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1841004.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3217 10 %RANDOM
Rwork0.199 ---
obs0.199 32178 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.1897 Å2 / ksol: 0.337045 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.4 Å20 Å20 Å2
2---0.61 Å20 Å2
3----4.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.72→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7632 0 24 309 7965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.72→2.89 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 493 9.3 %
Rwork0.254 4813 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOPPAR

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