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- PDB-1bxk: DTDP-GLUCOSE 4,6-DEHYDRATASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1bxk
TitleDTDP-GLUCOSE 4,6-DEHYDRATASE FROM E. COLI
ComponentsPROTEIN (DTDP-GLUCOSE 4,6-DEHYDRATASE)
KeywordsLYASE / EPIMERASE / DEHYDRATASE / DEHYDROGENASE
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / enterobacterial common antigen biosynthetic process / nucleotide-sugar metabolic process / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process
Similarity search - Function
dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / dTDP-glucose 4,6-dehydratase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsThoden, J.B. / Hegeman, A.D. / Frey, P.A. / Holden, H.M.
CitationJournal: Protein Sci.
Title: Molecular Structure of Dtdp-Glucose 4,6-Dehydratase from E. Coli
Authors: Thoden, J.B. / Hegeman, A.D. / Frey, P.A. / Holden, H.M.
History
DepositionOct 5, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: PROTEIN (DTDP-GLUCOSE 4,6-DEHYDRATASE)
B: PROTEIN (DTDP-GLUCOSE 4,6-DEHYDRATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7344
Polymers79,4072
Non-polymers1,3272
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-32 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.400, 109.200, 128.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (DTDP-GLUCOSE 4,6-DEHYDRATASE)


Mass: 39703.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P27830, dTDP-glucose 4,6-dehydratase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58 %
Crystal growpH: 6 / Details: 15% PEG 8000 100 MM K/MES PH 6.0

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Oct 15, 1997 / Details: GOBEL MIRRORS
RadiationMonochromator: GOBEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 73785 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.6 / % possible all: 86

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Processing

Software
NameVersionClassification
TNT5Erefinement
XDSdata reduction
XSCALIBREdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.195 --
all0.195 73774 -
obs-73774 96.3 %
Solvent computationSolvent model: TNT / Bsol: 325.9 Å2 / ksol: 0.857 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5409 0 88 359 5856
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01483662.3
X-RAY DIFFRACTIONt_angle_deg2.338110643.25
X-RAY DIFFRACTIONt_dihedral_angle_d16.52152600
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0071369.75
X-RAY DIFFRACTIONt_gen_planes0.012150211.5
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.3651095

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