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- PDB-3ehe: Crystal structure of UDP-glucose 4 epimerase (galE-1) from Archae... -

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Basic information

Entry
Database: PDB / ID: 3ehe
TitleCrystal structure of UDP-glucose 4 epimerase (galE-1) from Archaeoglobus fulgidus
ComponentsUDP-glucose 4-epimerase (GalE-1)
KeywordsISOMERASE / PSI-II / NYSGXRC / 11140g / galE-1 / UDP-glucose 4 epimerase / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


catalytic activity / nucleotide binding
Similarity search - Function
UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / 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 / UDP-glucose 4-epimerase (GalE-1)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of galE-1 from Archaeoglobus fulgidus
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionSep 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose 4-epimerase (GalE-1)
B: UDP-glucose 4-epimerase (GalE-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8714
Polymers70,5442
Non-polymers1,3272
Water3,513195
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-29 kcal/mol
Surface area25090 Å2
MethodPISA
2
A: UDP-glucose 4-epimerase (GalE-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9352
Polymers35,2721
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: UDP-glucose 4-epimerase (GalE-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9352
Polymers35,2721
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.574, 55.529, 89.634
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UDP-glucose 4-epimerase (GalE-1)


Mass: 35271.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_0361 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3(RIPL) / References: UniProt: O29886
#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.: 195 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 25% Ethylene Glycol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 20, 2008 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 54749 / Num. obs: 54749 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 1 / Num. unique all: 5335 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
Cootmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD
Starting model: None

Resolution: 1.87→34.46 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 83860.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1496 3 %RANDOM
Rwork0.253 ---
obs0.253 49719 90.5 %-
all-54749 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9707 Å2 / ksol: 0.349152 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.73 Å20 Å2-0.14 Å2
2--9.33 Å20 Å2
3----5.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 1.87→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 88 195 4863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 1.87→1.99 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 216 3.4 %
Rwork0.401 6185 -
obs--70.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramnad.top
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4nad.param

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