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- PDB-2b69: Crystal Structure of Human UDP-glucoronic acid decarboxylase -

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Basic information

Entry
Database: PDB / ID: 2b69
TitleCrystal Structure of Human UDP-glucoronic acid decarboxylase
ComponentsUDP-glucuronate decarboxylase 1
KeywordsLYASE / UDP-glucoronic acid decarboxylase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


UDP-glucuronate decarboxylase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / D-xylose metabolic process / Golgi cisterna membrane / catalytic complex / NAD+ binding / protein homodimerization activity / extracellular exosome / identical protein binding / cytoplasm
Similarity search - Function
UDP-glucuronate decarboxylase N-terminal / UDP-glucuronic acid decarboxylase / UDP-glucuronate decarboxylase N-terminal / 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 ...UDP-glucuronate decarboxylase N-terminal / UDP-glucuronic acid decarboxylase / UDP-glucuronate decarboxylase N-terminal / 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 / UDP-glucuronic acid decarboxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.21 Å
AuthorsUgochukwu, E. / Dubinina, E. / Kavanagh, K. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human UDP-glucoronic acid decarboxylase
Authors: Ugochukwu, E. / Dubinina, E. / Kavanagh, K. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / von Delft, F. / Oppermann, U.
History
DepositionSep 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucuronate decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6804
Polymers39,2081
Non-polymers1,4723
Water6,359353
1
A: UDP-glucuronate decarboxylase 1
hetero molecules

A: UDP-glucuronate decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3608
Polymers78,4172
Non-polymers2,9436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area8060 Å2
ΔGint-52 kcal/mol
Surface area23130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.000, 45.000, 85.000
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein UDP-glucuronate decarboxylase 1


Mass: 39208.363 Da / Num. of mol.: 1 / Fragment: UXS1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UXS1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) Methionine auxotroph / References: UniProt: Q8NBZ7, UDP-glucuronate decarboxylase
#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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.3 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: PEG3350, Zn (ac)2, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→42.37 Å / Num. obs: 93023 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.2→1.26 Å / % possible all: 58.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.21→40 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.333 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16203 4473 5 %RANDOM
Rwork0.13418 ---
all0.13559 84968 --
obs0.13559 84968 84.92 %-
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: 12.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.07 Å2
2--0.22 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.21→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 94 353 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222675
X-RAY DIFFRACTIONr_bond_other_d0.0010.022374
X-RAY DIFFRACTIONr_angle_refined_deg1.50623667
X-RAY DIFFRACTIONr_angle_other_deg0.87735545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70224.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35315439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2341515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02512
X-RAY DIFFRACTIONr_nbd_refined0.2140.2367
X-RAY DIFFRACTIONr_nbd_other0.1720.22040
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21192
X-RAY DIFFRACTIONr_nbtor_other0.0760.21157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.217
X-RAY DIFFRACTIONr_mcbond_it3.84151910
X-RAY DIFFRACTIONr_mcbond_other2.3565648
X-RAY DIFFRACTIONr_mcangle_it3.95172584
X-RAY DIFFRACTIONr_scbond_it5.24591211
X-RAY DIFFRACTIONr_scangle_it6.62111070
X-RAY DIFFRACTIONr_rigid_bond_restr2.68235826
X-RAY DIFFRACTIONr_sphericity_free7.813353
X-RAY DIFFRACTIONr_sphericity_bonded4.2934973
LS refinement shellResolution: 1.21→1.241 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 76 -
Rwork0.277 1604 -
obs--21.93 %

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