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- PDB-4lk3: Crystal structure of Human UDP-xylose synthase R236A substitution -

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Basic information

Entry
Database: PDB / ID: 4lk3
TitleCrystal structure of Human UDP-xylose synthase R236A substitution
ComponentsUDP-glucuronic acid decarboxylase 1
KeywordsLYASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / DECARBOXYLASE / MEMBRANE / ROSSMANN FOLD
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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYROPHOSPHATE 2- / URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-glucuronic acid decarboxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWalsh Jr., R.M. / Polizzi, S.J. / Wood, Z.A.
CitationJournal: Biochemistry / Year: 2015
Title: Man o' war mutation in UDP-alpha-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation.
Authors: Walsh Jr., R.M. / Polizzi, S.J. / Kadirvelraj, R. / Howard, W.W. / Wood, Z.A.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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-glucuronic acid decarboxylase 1
B: UDP-glucuronic acid decarboxylase 1
C: UDP-glucuronic acid decarboxylase 1
D: UDP-glucuronic acid decarboxylase 1
E: UDP-glucuronic acid decarboxylase 1
F: UDP-glucuronic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,09633
Polymers227,0286
Non-polymers10,06727
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25110 Å2
ΔGint-244 kcal/mol
Surface area64920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.570, 92.070, 290.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
UDP-glucuronic acid decarboxylase 1 / UDP-glucuronate decarboxylase 1 / UGD / UXS-1


Mass: 37838.059 Da / Num. of mol.: 6 / Fragment: UNP residues 85-420 / Mutation: R236A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNQ2538/PRO6079, UXS, UXS1 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NBZ7, UDP-glucuronate decarboxylase

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Non-polymers , 6 types, 101 molecules

#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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H22N2O18P2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.47 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 293 K / pH: 5.4
Details: 0.1 M ammonium sulfate, 0.1 M succinate, 10% DMSO, pH 5.4, Vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 65871 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 11.87 % / Biso Wilson estimate: 60.46 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.9
Reflection shellResolution: 2.64→2.71 Å / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 2.7 / % possible all: 86.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B69
Resolution: 2.64→36.37 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 3330 5.06 %
Rwork0.198 --
obs0.2 65842 98.4 %
all-66963 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.375 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.64→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12727 0 633 74 13434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113624
X-RAY DIFFRACTIONf_angle_d1.48118515
X-RAY DIFFRACTIONf_dihedral_angle_d19.1415084
X-RAY DIFFRACTIONf_chiral_restr0.0782089
X-RAY DIFFRACTIONf_plane_restr0.0092279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.67810.37511250.31831981X-RAY DIFFRACTION77
2.6781-2.71810.41691140.28172593X-RAY DIFFRACTION98
2.7181-2.76050.27391350.24752589X-RAY DIFFRACTION100
2.7605-2.80580.31181130.24182620X-RAY DIFFRACTION98
2.8058-2.85410.28671540.22962570X-RAY DIFFRACTION100
2.8541-2.9060.25231630.21642548X-RAY DIFFRACTION98
2.906-2.96190.29531500.22522613X-RAY DIFFRACTION100
2.9619-3.02230.31461290.2182578X-RAY DIFFRACTION99
3.0223-3.0880.26571370.23052597X-RAY DIFFRACTION99
3.088-3.15980.30071620.22772581X-RAY DIFFRACTION99
3.1598-3.23880.28211170.22162616X-RAY DIFFRACTION99
3.2388-3.32630.26111390.20222619X-RAY DIFFRACTION100
3.3263-3.42410.24081380.20452620X-RAY DIFFRACTION99
3.4241-3.53450.24041370.20632624X-RAY DIFFRACTION99
3.5345-3.66070.27061500.2152611X-RAY DIFFRACTION99
3.6607-3.80710.22571190.20852640X-RAY DIFFRACTION99
3.8071-3.98020.27231510.19252642X-RAY DIFFRACTION100
3.9802-4.18980.2261250.18522648X-RAY DIFFRACTION100
4.1898-4.45180.17661410.16452637X-RAY DIFFRACTION100
4.4518-4.79490.19691350.15952668X-RAY DIFFRACTION100
4.7949-5.27610.22631500.17222660X-RAY DIFFRACTION100
5.2761-6.03650.26051390.18062685X-RAY DIFFRACTION100
6.0365-7.5940.23971480.19112749X-RAY DIFFRACTION100
7.594-36.37220.22251590.19592823X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.8761-0.6098-0.55783.53570.14183.01190.2080.82260.1408-1.0202-0.0968-0.2332-0.2051-0.2255-0.00040.75970.18490.02610.89850.21530.515354.651616.454913.8319
21.3877-0.86910.58392.55540.32884.61110.10280.88840.5939-0.4779-0.1-0.1734-0.18930.6030.03610.39240.0660.03530.61140.19040.439155.856613.074228.0005
31.4292-1.4446-0.50122.90570.76874.04170.14940.47610.1348-0.3294-0.0415-0.48720.29910.29130.00610.51390.10980.01010.68610.07940.436260.04284.727524.6903
42.47-0.7147-0.8343.69170.10532.35580.08430.49470.227-0.6692-0.0737-1.34370.20460.75680.02370.82860.23520.21031.07520.10770.855576.0655.499513.9191
52.8799-0.9420.58743.119-0.20142.75040.04-0.38920.27560.22570.06110.1096-0.2955-0.1610.00230.28020.01010.03380.51120.02480.482849.117513.088360.2793
62.2972-1.46940.36541.6480.71693.66860.28850.16310.154-0.0956-0.1934-0.22960.05450.32680.00360.28780.01260.04580.53540.10170.461357.904710.772346.1585
72.5576-0.5637-0.28861.0685-1.49991.85790.00110.0961-0.3261-0.22770.18140.00240.30930.2121-0.01520.30410.0207-0.06290.48250.05510.495259.2836-4.56257.4879
82.56920.70110.23463.4081-0.84412.1554-0.0087-0.1605-0.4797-0.18470.0858-0.06660.47360.184-0.00890.37190.0424-0.04830.42230.0640.547258.1634-11.269963.2043
93.1923-0.4741-0.46653.5551-0.83121.96050.0960.1848-0.7052-0.3654-0.2125-0.0060.2213-0.0349-0.03130.24850.03670.01640.57030.00110.56628.21723.679948.7932
102.14160.5872-0.12723.80821.63861.480.15290.1227-0.21490.15590.0411-0.05380.1885-0.0433-0.12340.26220.0763-0.00720.55220.07320.435624.91117.695350.4713
112.34140.4479-0.94782.9822-1.05070.96540.18150.02520.01880.1549-0.15720.3547-0.2656-0.3014-0.00730.2427-0.0018-0.03550.6010.00010.561816.406414.509954.7569
121.1396-0.5419-0.2211.3623-0.56912.63650.0017-0.4516-0.23760.3215-0.08120.27530.0086-0.4371-0.02540.3378-0.13460.03770.76840.06130.684216.36662.838570.2709
132.4568-0.8864-0.46423.4651-0.25533.3430.36690.30850.5927-0.561-0.2732-0.2935-1.0708-0.16280.01640.66390.10070.11490.46540.13170.504226.062150.608646.3392
141.75991.3538-0.68453.99840.26032.8625-0.08210.42960.3837-0.5705-0.08520.4482-0.4491-0.37820.04440.320.1427-0.00910.41110.11370.420323.472336.643149.2423
152.6434-0.4447-0.79073.23070.01192.7227-0.13-0.0725-0.2144-0.071-0.02560.19820.0704-0.4239-0.02510.29780.0749-0.01440.44570.03920.36122.781935.235659.7737
160.8996-1.166-0.38592.7443-0.46652.33180.41040.41960.0481-0.4888-0.31080.4729-0.365-0.6093-0.11490.53690.2194-0.02020.6121-0.01490.490212.98145.340253.7952
171.7538-1.2113-0.96910.8366-0.16242.82650.1776-0.07330.0171-0.3011-0.00990.3241-0.6238-1.1086-0.03230.61640.23220.02190.72990.03430.60355.385148.209155.7982
182.25760.4539-0.70963.9026-0.78052.16070.20640.40090.4244-0.1748-0.21380.6783-0.6035-1.0096-0.00120.81770.55120.00311.37680.04080.8131-9.197452.181452.1025
192.9297-0.26121.52530.52730.27532.52130.01710.13530.3654-0.2227-0.12580.1164-0.7896-0.709-0.00010.77710.40750.04850.88650.04280.64856.681853.729455.1394
203.8517-1.64860.18532.07820.00093.68290.06940.53730.076-0.2307-0.12690.1112-0.4466-0.40820.00590.77860.20110.03210.69960.15270.482924.64743.07619.8506
212.1874-0.57790.36832.6263-0.62961.474-0.0010.36670.6507-0.2234-0.0430.0455-0.8426-0.282-0.02351.22320.36410.03761.03050.35490.860618.190662.837413.6541
222.31290.15130.27841.9133-0.29561.59390.01460.09050.2560.21110.0257-0.858-0.15250.8214-0.01810.75080.04230.00880.93540.24590.907464.730737.555424.1296
233.9662-0.01060.59362.4581-0.81111.95490.0650.23150.127-0.1574-0.1254-0.8506-0.08690.6258-0.10350.83150.12160.0260.65270.22790.778450.70441.046721.8764
241.7982-0.1781-0.35991.5683-0.67491.13050.03660.37890.5069-0.28930.0213-0.3808-1.02640.0137-0.05271.1179-0.00140.04130.71550.18870.904854.416349.142117.1338
250.6951-0.2666-0.171.4356-0.87120.4419-0.20380.39070.3975-0.4316-0.3391-0.1244-0.29590.53890.03290.9838-0.10170.10780.98780.35131.293464.313649.17045.7999
261.9708-0.0052-0.51261.3013-0.22961.81580.18790.64630.7898-0.776-0.3603-0.6055-0.35390.3230.02491.3481-0.04290.34591.19530.41531.355169.504447.36910.9349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 88 : 154 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 155 : 192 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 193 : 272 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 273 : 399 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 88 : 154 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 155 : 249 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 250 : 327 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 328 : 399 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 88 : 154 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 155 : 193 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 194 : 272 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 273 : 399 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 88 : 154 )
14X-RAY DIFFRACTION14CHAIN D AND (RESID 155 : 193 )
15X-RAY DIFFRACTION15CHAIN D AND (RESID 194 : 249 )
16X-RAY DIFFRACTION16CHAIN D AND (RESID 250 : 272 )
17X-RAY DIFFRACTION17CHAIN D AND (RESID 273 : 327 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 328 : 350 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 351 : 399 )
20X-RAY DIFFRACTION20CHAIN E AND (RESID 88 : 272 )
21X-RAY DIFFRACTION21CHAIN E AND (RESID 273 : 399 )
22X-RAY DIFFRACTION22CHAIN F AND (RESID 88 : 154 )
23X-RAY DIFFRACTION23CHAIN F AND (RESID 155 : 192 )
24X-RAY DIFFRACTION24CHAIN F AND (RESID 193 : 272 )
25X-RAY DIFFRACTION25CHAIN F AND (RESID 273 : 327 )
26X-RAY DIFFRACTION26CHAIN F AND (RESID 328 : 399 )

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