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- PDB-1x8d: Crystal structure of E. coli YiiL protein containing L-rhamnose -

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Basic information

Entry
Database: PDB / ID: 1x8d
TitleCrystal structure of E. coli YiiL protein containing L-rhamnose
ComponentsHypothetical protein yiiLHypothesis
KeywordsBIOSYNTHETIC PROTEIN / Mutarotase / L-rhamnose
Function / homology
Function and homology information


L-rhamnose mutarotase / L-rhamnose mutarotase activity / rhamnose catabolic process / racemase and epimerase activity, acting on carbohydrates and derivatives / cytoplasm
Similarity search - Function
L-rhamnose mutarotase / Rhamnose/fucose mutarotase / L-rhamnose mutarotase / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-RHAMNOSE / L-rhamnose mutarotase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsRyu, K.S. / Kim, J.I. / Cho, S.J. / Park, D. / Park, C. / Lee, J.O. / Choi, B.S.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Insights into the Monosaccharide Specificity of Escherichia coli Rhamnose Mutarotase
Authors: Ryu, K.S. / Kim, J.I. / Cho, S.J. / Park, D. / Park, C. / Cheong, H.K. / Lee, J.O. / Choi, B.S.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 8, 2018Group: Data collection / Category: diffrn_source / struct_biol / Item: _diffrn_source.source
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein yiiL
B: Hypothetical protein yiiL
C: Hypothetical protein yiiL
D: Hypothetical protein yiiL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7728
Polymers49,1154
Non-polymers6574
Water9,044502
1
A: Hypothetical protein yiiL
B: Hypothetical protein yiiL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8864
Polymers24,5582
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-13 kcal/mol
Surface area10300 Å2
MethodPISA
2
C: Hypothetical protein yiiL
D: Hypothetical protein yiiL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8864
Polymers24,5582
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-13 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.358, 51.311, 80.492
Angle α, β, γ (deg.)90.00, 107.82, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological functional uint is a dimer for the rhamnose mutarotase acitivity

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Components

#1: Protein
Hypothetical protein yiiL / Hypothesis / L-rhamnose mutarotase


Mass: 12278.864 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32156
#2: Sugar
ChemComp-RNS / L-RHAMNOSE / Rhamnose


Type: L-saccharide / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: sodium citrate, L-rhamnose, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
20.9793, 0.9788, 0.9686
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATENov 20, 2003
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97931
30.97881
40.96861
ReflectionResolution: 1.8→20 Å / Num. all: 51664 / Num. obs: 41131 / % possible obs: 79.6 %
Reflection shellResolution: 1.94→2.03 Å / % possible all: 65.5

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Processing

Software
NameClassification
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2787 1758 Random
Rwork0.2351 --
all-51664 -
obs-41131 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 44 502 4002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.3062

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