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- PDB-4wok: Crystal structure of UDP-glucose 4-epimerase from Brucella ovis i... -

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Basic information

Entry
Database: PDB / ID: 4wok
TitleCrystal structure of UDP-glucose 4-epimerase from Brucella ovis in complex with NAD
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / SSGCID / Brucella ovis / brucellosis / UDP-glucose 4-epimerase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / 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 / PHOSPHATE ION / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of UDP-glucose 4-epimerase from Brucella ovis in complex with NAD
Authors: SSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Derived calculations
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,0834
Polymers36,2591
Non-polymers8243
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.480, 86.460, 126.850
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-504-

HOH

21A-538-

HOH

31A-577-

HOH

41A-582-

HOH

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Components

#1: Protein UDP-glucose 4-epimerase


Mass: 36258.766 Da / Num. of mol.: 1 / Fragment: BrovA.00085.C / Mutation: V68A, Y321H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (bacteria) / Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: galE-1, BOV_A0474 / Plasmid: BrovA.00085.c.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5VUK4, UniProt: A0A0H3ASR6*PLUS, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MCSG1 screen, g11 40% PEG 300, 100mM NaPhosphate pH 4.2; BrovA.00085.c.B1.PS02133 at 15mg/ml, supplemented with 2.5mM NAD; direct cryo; tray 257996g11, puck kpy8-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 6, 2010
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 36273 / Num. obs: 36182 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 25.87 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.04 / Rsym value: 0.035 / Χ2: 0.953 / Net I/σ(I): 26.39 / Num. measured all: 170114
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.85-1.92.80.7680.5562.017333264826250.69399.1
1.9-1.950.8540.3743.17593261226000.46299.5
1.95-2.010.890.3243.77476248524760.39699.6
2.01-2.070.940.225.527597243524310.26799.8
2.07-2.140.960.1857.338224238523770.21999.7
2.14-2.210.9810.14710.359397228322790.16999.8
2.21-2.290.9870.11413.859520219821950.1399.9
2.29-2.390.9910.10115.549751215621510.11599.8
2.39-2.490.9950.07320.649659203920360.08299.9
2.49-2.620.9970.06523.379971197319710.07399.9
2.62-2.760.9980.05727.610427189018870.06399.8
2.76-2.930.9990.04934.2711362175717550.05399.9
2.93-3.130.9990.03842.0411146165916590.042100
3.13-3.380.9990.02952.4710541157515750.031100
3.38-3.710.02465.929618143614360.026100
3.7-4.1410.02173.068800132413240.023100
4.14-4.7810.01979.627709117011700.021100
4.78-5.8510.0276.9664589919910.021100
5.85-8.2710.0277.0849667877870.022100
8.270.9990.01987.5925664704570.02197.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å38.07 Å
Translation2 Å38.07 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALE2.5.6data scaling
PHASERphasing
ARPmodel building
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2c20, modified with CCP4 program CHAINSAW

2c20


Resolution: 1.85→43.23 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 1810 5 %RANDOM SELECTION
Rwork0.167 34369 --
obs0.1686 36179 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.87 Å2 / Biso mean: 35.5764 Å2 / Biso min: 13.08 Å2
Refinement stepCycle: final / Resolution: 1.85→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 50 242 2710
Biso mean--28.88 41.1 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082612
X-RAY DIFFRACTIONf_angle_d1.1363583
X-RAY DIFFRACTIONf_chiral_restr0.045406
X-RAY DIFFRACTIONf_plane_restr0.005468
X-RAY DIFFRACTIONf_dihedral_angle_d12.862924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.90010.35461380.28242603274199
1.9001-1.9560.28641360.242825892725100
1.956-2.01910.28381420.221226042746100
2.0191-2.09130.25391300.201226302760100
2.0913-2.1750.22421380.188725982736100
2.175-2.2740.2131410.175326282769100
2.274-2.39390.2141410.176126432784100
2.3939-2.54380.18621330.165326232756100
2.5438-2.74020.21741400.16926432783100
2.7402-3.01590.20951370.170326472784100
3.0159-3.45220.19321420.166426772819100
3.4522-4.34870.18061430.137826842827100
4.3487-43.24180.14871490.144628002949100
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)
11.7863-0.0716-0.38781.43680.44631.54890.03350.2290.0118-0.1922-0.1893-0.1627-0.11950.46530.12040.1664-0.00110.01180.27370.11760.200512.24166.029942.9859
21.90210.2229-0.41211.05330.09362.04750.0420.05370.3131-0.028-0.1987-0.0739-0.33170.06670.14620.209-0.0247-0.03120.17830.05990.21345.587315.287155.3578
30.29430.3625-0.15280.798-0.05121.5331-0.06120.30210.3274-0.1124-0.09550.0026-0.44030.13560.05790.3496-0.0152-0.03980.31630.18930.36183.914622.110839.9922
40.08820.0514-0.13460.38130.12470.82380.00190.21430.2247-0.1319-0.0797-0.0418-0.4651-0.0314-0.17650.475-0.0052-0.08840.47080.26980.44510.531126.785333.2395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 56 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 161 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 260 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 261 through 327 )A0

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