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- PDB-1jov: Crystal Structure Analysis of HI1317 -

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Basic information

Entry
Database: PDB / ID: 1jov
TitleCrystal Structure Analysis of HI1317
ComponentsHI1317
KeywordsUNKNOWN FUNCTION / hypothetical protein / Structure 2 Function Project / S2F / Structural Genomics
Function / homology
Function and homology information


glucose-6-phosphate 1-epimerase / glucose-6-phosphate 1-epimerase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glucose-6-phosphate 1-epimerase / Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Glucose-6-phosphate 1-epimerase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.57 Å
AuthorsBonander, N. / Tordova, M. / Howard, A.J. / Eisenstein, E. / Gilliland, G. / Structure 2 Function Project (S2F)
CitationJournal: TO BE PUBLISHED
Title: Crystal 1.57-A Crystal Structure of HI1317
Authors: Bonander, N. / Tordova, M. / Howard, A.J. / Eisenstein, E. / Gilliland, G.
History
DepositionJul 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HI1317
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1094
Polymers30,7691
Non-polymers3403
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.540, 38.860, 92.360
Angle α, β, γ (deg.)90.00, 110.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21A-540-

HOH

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Components

#1: Protein HI1317


Mass: 30769.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI1317 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RP27
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.19 Å3/Da / Density % sol: 43.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 30% 4K-PEG, 0.2M LiSO4, 0.1 M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: BRUKER / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→15 Å / Num. obs: 33851 / % possible obs: 94.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 13.4
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.1 / % possible all: 81.7

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Processing

Software
NameClassification
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
RefinementResolution: 1.57→15 Å / SU B: 2.77 / SU ML: 0.097 / ESU R: 0.111 / ESU R Free: 0.116
RfactorNum. reflection% reflection
Rfree0.26 --
Rwork0.208 --
obs-33851 94.3 %
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20.11 Å2
2--3.08 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.57→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 21 235 2517

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