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- PDB-4twr: Structure of UDP-glucose 4-epimerase from Brucella abortus -

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Basic information

Entry
Database: PDB / ID: 4twr
TitleStructure of UDP-glucose 4-epimerase from Brucella abortus
ComponentsNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / 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
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHoranyi, P.S. / Abendroth, J. / Lorimer, D. / Edwards, T. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structure of UDP-glucose 4-epimerase from Brucella melitensis
Authors: Horanyi, P.S. / Abendroth, J. / Lorimer, D. / Edwards, T.
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9883
Polymers36,2591
Non-polymers7292
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.600, 86.110, 126.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-538-

HOH

31A-540-

HOH

41A-569-

HOH

51A-573-

HOH

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Components

#1: Protein NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase


Mass: 36258.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 2308 / Gene: galE-2, BAB2_0694
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q2YKG6, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 200mM Ammonium Acetate, 25% PEG 3350, 100mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 11, 2014
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33325 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.18 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.053 / Χ2: 0.979 / Net I/σ(I): 25.79 / Num. measured all: 247010
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.950.9230.5193.6618248244524430.55799.9
1.95-20.9380.4324.5417700237023700.464100
2-2.060.9660.3235.9817231230323030.347100
2.06-2.120.9750.2567.6216824224822480.275100
2.12-2.190.9840.2099.2216447219321930.225100
2.19-2.270.9890.1612.0415584208020800.172100
2.27-2.360.9920.13114.7715287203720370.14100
2.36-2.450.9960.09818.914832197919790.105100
2.45-2.560.9970.08222.113977186918690.088100
2.56-2.690.9980.06826.1913651181718170.073100
2.69-2.830.9980.05630.6312817171217120.06100
2.83-30.9990.04735.7612184163516350.051100
3-3.210.9990.03942.5511414153915380.04299.9
3.21-3.470.9990.03251.1410596143614360.035100
3.47-3.80.9990.02957.999714132413240.031100
3.8-4.250.9990.02661.618876122212210.02899.9
4.25-4.9110.02466.387662106110610.026100
4.91-6.0110.02464.7265699279270.026100
6.01-8.50.9990.02365.7649787287280.025100
8.50.9990.02366.7424194294040.02594.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1769)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.992 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 1999 6 %
Rwork0.1785 31320 -
obs0.1806 33319 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.54 Å2 / Biso mean: 42.1223 Å2 / Biso min: 15.26 Å2
Refinement stepCycle: final / Resolution: 1.9→27.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 45 205 2670
Biso mean--35.98 43.44 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0392549
X-RAY DIFFRACTIONf_angle_d1.1183475
X-RAY DIFFRACTIONf_chiral_restr0.044393
X-RAY DIFFRACTIONf_plane_restr0.005454
X-RAY DIFFRACTIONf_dihedral_angle_d12.943892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94750.34281400.245922182358100
1.9475-2.00010.26031410.236721982339100
2.0001-2.0590.29331400.229422012341100
2.059-2.12540.27511420.221422192361100
2.1254-2.20130.27531410.207522102351100
2.2013-2.28940.25291410.199522042345100
2.2894-2.39360.25371430.194622432386100
2.3936-2.51970.20981420.18722222364100
2.5197-2.67740.26161430.187322372380100
2.6774-2.8840.21371420.190622242366100
2.884-3.17380.20541430.190922412384100
3.1738-3.63220.20191440.176522562400100
3.6322-4.5730.17161450.145822762421100
4.573-27.99510.17791520.14872371252399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6440.31650.75321.8763-0.39931.5535-0.00350.5538-0.0955-0.0642-0.2030.17150.1203-0.45230.19440.23020.0111-0.00510.3204-0.13130.2327-11.332-4.591-18.678
20.6580.74920.36381.47990.45271.8148-0.01440.3418-0.686-0.0779-0.1640.02280.3453-0.02430.14210.3217-0.00920.05120.2358-0.10140.386-4.88-16.431-8.907
31.0759-0.5477-0.03543.82054.62977.0347-0.08170.2177-0.73080.0421-0.16940.25630.5286-0.48360.25840.3188-0.09170.06040.2172-0.0770.4228-12.657-18.589-2.903
40.81620.1587-0.50410.51610.06431.3616-0.06290.4453-0.5045-0.0871-0.0522-0.0040.42440.06140.08030.4540.00380.0830.5545-0.53590.5377-1.807-22.999-26.111
51.24930.0499-0.58551.3037-0.41973.2678-0.05060.0343-0.16470.1158-0.14730.06350.16850.12910.13980.64850.02440.13120.7927-0.43440.627610.882-27.749-30.965
60.12120.19210.42641.70480.88841.3873-0.08320.8229-0.7847-0.4928-0.14290.10990.6563-0.22230.18280.4065-0.0540.08910.3901-0.69510.4092-7.431-23.279-27.041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 11:64)A11 - 64
2X-RAY DIFFRACTION2(CHAIN A AND RESID 65:149)A65 - 149
3X-RAY DIFFRACTION3(CHAIN A AND RESID 150:169)A150 - 169
4X-RAY DIFFRACTION4(CHAIN A AND RESID 170:268)A170 - 268
5X-RAY DIFFRACTION5(CHAIN A AND RESID 269:289)A269 - 289
6X-RAY DIFFRACTION6(CHAIN A AND RESID 290:327)A290 - 327

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