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- PDB-3enk: 1.9A crystal structure of udp-glucose 4-epimerase from burkholder... -

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Basic information

Entry
Database: PDB / ID: 3enk
Title1.9A crystal structure of udp-glucose 4-epimerase from burkholderia pseudomallei
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / BURKHOLDERIA / PSEUDOMALLEI / UDP-GLUCOSE / EPIMERASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / NAD
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / nucleotide binding / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / 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 / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 1.9A crystal structure of udp-glucose 4-epimerase from burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 8, 2013Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 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

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Assembly

Deposited unit
A: UDP-glucose 4-epimerase
B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0086
Polymers74,5482
Non-polymers2,4594
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-39 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.860, 83.471, 82.576
Angle α, β, γ (deg.)90.000, 96.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-glucose 4-epimerase


Mass: 37274.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1710B / Gene: BURPS1710B_2458, BURPS1710b_3147, galE, MSRB / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JPI3, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 6000, 0.1M HEPES pH 7.0, 0.2M NaCl, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 73250 / % possible obs: 94.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.046 / Χ2: 1.993 / Net I/σ(I): 39.327
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.812.40.29951840.939167.2
1.81-1.8930.24968811.101189.4
1.89-1.973.60.19776311.188198.9
1.97-2.073.80.13777221.4231100
2.07-2.23.80.10177221.704199.9
2.2-2.383.80.08177172.11199.9
2.38-2.613.70.06777222.563199.8
2.61-2.993.70.05176672.53198.9
2.99-3.773.60.04475983.16197.8
3.77-503.60.03374062.315193.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.37 Å
Translation2.5 Å47.37 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.832 / SU B: 3.381 / SU ML: 0.101 / SU R Cruickshank DPI: 0.156 / SU Rfree: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2988 5 %RANDOM
Rwork0.194 ---
obs0.197 59681 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.21 Å2 / Biso mean: 36.78 Å2 / Biso min: 22.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å2-1.52 Å2
2--0.02 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 160 367 5758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225535
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9937561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70522.675243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63415855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6141554
X-RAY DIFFRACTIONr_chiral_restr0.1090.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024196
X-RAY DIFFRACTIONr_nbd_refined0.20.22681
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2440
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.214
X-RAY DIFFRACTIONr_mcbond_it0.8231.53470
X-RAY DIFFRACTIONr_mcangle_it1.33625447
X-RAY DIFFRACTIONr_scbond_it2.13832335
X-RAY DIFFRACTIONr_scangle_it3.3934.52110
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 210 -
Rwork0.233 4153 -
all-4363 -
obs--99.2 %

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