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- PDB-1orr: Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD ... -

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Basic information

Entry
Database: PDB / ID: 1orr
TitleCrystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP
ComponentsCDP-tyvelose-2-epimerase
KeywordsISOMERASE / Rossmann fold / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


CDP-paratose 2-epimerase / CDP-abequose epimerase activity / lipopolysaccharide biosynthetic process
Similarity search - Function
GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / CDP-paratose 2-epimerase
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsKoropatkin, N.M. / Liu, H. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: High Resolution X-ray Structure of Tyvelose Epimerase from Salmonella typhi
Authors: Koropatkin, N.M. / Liu, H.W. / Holden, H.M.
History
DepositionMar 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: CDP-tyvelose-2-epimerase
B: CDP-tyvelose-2-epimerase
C: CDP-tyvelose-2-epimerase
D: CDP-tyvelose-2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,81912
Polymers156,5524
Non-polymers4,2668
Water19,4381079
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CDP-tyvelose-2-epimerase
D: CDP-tyvelose-2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4096
Polymers78,2762
Non-polymers2,1334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-42 kcal/mol
Surface area24470 Å2
MethodPISA, PQS
3
A: CDP-tyvelose-2-epimerase
C: CDP-tyvelose-2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4096
Polymers78,2762
Non-polymers2,1334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-41 kcal/mol
Surface area24290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.000, 168.100, 89.600
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CDP-tyvelose-2-epimerase


Mass: 39138.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: RFBE OR STY2298 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P14169, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1079 / 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: 2.06 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 8000, succinate, tetramethylammonium chloride, CDP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113 mg/mlprotein1drop
220 mMHEPPS1reservoirpH8.0
3200 mM1reservoirNaCl
45 mMCDP1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 4, 2002 / Details: mirrors
RadiationMonochromator: double crystal Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. all: 225494 / Num. obs: 225494 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.061 / Net I/σ(I): 40.8
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 21022 / Rsym value: 0.212 / % possible all: 89.2
Reflection
*PLUS
Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 89.2 % / Redundancy: 2.8 % / Num. unique obs: 21022 / Rmerge(I) obs: 0.212

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
TNTrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 22493 -random
Rwork0.178 ---
all0.179 225493 --
obs0.179 225493 95.2 %-
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10617 0 276 1079 11972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.23
X-RAY DIFFRACTIONt_dihedral_angle_d16.2
Refinement
*PLUS
Num. reflection obs: 203000
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.2
X-RAY DIFFRACTIONt_planar_d0.005
X-RAY DIFFRACTIONt_plane_restr0.01

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