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- PDB-2c20: CRYSTAL STRUCTURE OF UDP-GLUCOSE 4-EPIMERASE -

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Basic information

Entry
Database: PDB / ID: 2c20
TitleCRYSTAL STRUCTURE OF UDP-GLUCOSE 4-EPIMERASE
ComponentsUDP-GLUCOSE 4-EPIMERASE
KeywordsISOMERASE / CARBOHYDRATE METABOLISM / GALACTOSE METABOLISM / NAD / SPINE
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / nucleotide binding / metal ion binding
Similarity search - Function
UDP-glucose 4-epimerase / 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 / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLebedev, A.A. / Moroz, O.V. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
CitationJournal: To be Published
Title: Crystal Structure of Udp-Glucose 4-Epimerase from Bacillus Anthracis at 2.7A Resolution
Authors: Lebedev, A.A. / Moroz, O.V. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionSep 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: UDP-GLUCOSE 4-EPIMERASE
B: UDP-GLUCOSE 4-EPIMERASE
C: UDP-GLUCOSE 4-EPIMERASE
D: UDP-GLUCOSE 4-EPIMERASE
E: UDP-GLUCOSE 4-EPIMERASE
F: UDP-GLUCOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,10618
Polymers221,7336
Non-polymers4,37312
Water4,216234
1
A: UDP-GLUCOSE 4-EPIMERASE
B: UDP-GLUCOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3696
Polymers73,9112
Non-polymers1,4584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: UDP-GLUCOSE 4-EPIMERASE
D: UDP-GLUCOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3696
Polymers73,9112
Non-polymers1,4584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: UDP-GLUCOSE 4-EPIMERASE
F: UDP-GLUCOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3696
Polymers73,9112
Non-polymers1,4584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.165, 136.165, 248.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein
UDP-GLUCOSE 4-EPIMERASE


Mass: 36955.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q81K34, UniProt: A0A6L8PTV5*PLUS, UDP-glucose 4-epimerase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY INVOLVES UDP-GLUCOSE = UDP-GALACTOSE.

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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: 3 Å3/Da / Density % sol: 58.5 %
Crystal growpH: 6.5
Details: 22% PEG 2K MME, 0.2M CALCIUM ACETATE, 0.1 MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00806
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00806 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 70638 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GY8

1gy8


Resolution: 2.7→25.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 39.3 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2747 5.3 %RANDOM
Rwork0.205 ---
obs0.208 48909 73.1 %-
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 mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.39 Å20 Å2
2---0.77 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15546 0 270 234 16050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.96522020
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58151968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6524.924792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.096152652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0461572
X-RAY DIFFRACTIONr_chiral_restr0.0990.22406
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212396
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.27964
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.210867
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2705
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5781.59976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.997215738
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47137030
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.314.56282
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.367 414
Rwork0.283 3216

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