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- PDB-3tov: The crystal structure of the glycosyl transferase family 9 from V... -

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Basic information

Entry
Database: PDB / ID: 3tov
TitleThe crystal structure of the glycosyl transferase family 9 from Veillonella parvula DSM 2008
ComponentsGlycosyl transferase family 9
KeywordsTRANSFERASE / glycosyl transferase family 9 / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyGlycosyl transferase, family 9 / Glycosyltransferase family 9 (heptosyltransferase) / glycosyltransferase activity / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Glycosyl transferase family 9
Function and homology information
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.983 Å
AuthorsTan, K. / Marshall, N. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the glycosyl transferase family 9 from Veillonella parvula DSM 2008
Authors: Tan, K. / Marshall, N. / Clancy, S. / Joachimiak, A.
History
DepositionSep 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase family 9
B: Glycosyl transferase family 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,89413
Polymers79,8382
Non-polymers1,05711
Water48627
1
A: Glycosyl transferase family 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3996
Polymers39,9191
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl transferase family 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4957
Polymers39,9191
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.708, 95.394, 121.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. The molecule is predicted to be monomeric.

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Components

#1: Protein Glycosyl transferase family 9


Mass: 39918.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_0760 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: D1BM34
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M Magnesium sulfate, 0.1M MES:NaOH., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918, 0.97932
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979321
ReflectionResolution: 2.983→41 Å / Num. all: 18816 / Num. obs: 18816 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 15.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.5 / Num. unique all: 929 / % possible all: 98.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.983→40.791 Å / SU ML: 0.81 / σ(F): 1.34 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 957 5.11 %random
Rwork0.1711 ---
all0.176 18739 --
obs0.176 18739 97.5 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.436 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.3506 Å2-0 Å20 Å2
2---18.8122 Å2-0 Å2
3---28.1628 Å2
Refinement stepCycle: LAST / Resolution: 2.983→40.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 55 27 5539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085626
X-RAY DIFFRACTIONf_angle_d1.1767636
X-RAY DIFFRACTIONf_dihedral_angle_d17.7842056
X-RAY DIFFRACTIONf_chiral_restr0.075852
X-RAY DIFFRACTIONf_plane_restr0.005971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.983-3.14020.39821230.26842371X-RAY DIFFRACTION93
3.1402-3.33690.3351380.22572535X-RAY DIFFRACTION99
3.3369-3.59440.2841360.17792553X-RAY DIFFRACTION99
3.5944-3.95590.26811550.16092544X-RAY DIFFRACTION99
3.9559-4.52760.21381360.13542561X-RAY DIFFRACTION99
4.5276-5.70190.25581450.14882565X-RAY DIFFRACTION98
5.7019-40.79530.24351240.17182653X-RAY DIFFRACTION96
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)
14.1416-1.120.08273.2191-0.18533.67820.15660.3169-0.449-0.2989-0.2496-0.35810.25290.53980.04180.25060.1523-0.03050.33780.10150.541440.744417.871940.1084
28.9257-2.28663.41035.41651.00565.93140.22150.3624-1.0379-0.0143-0.1321-0.30971.14660.3852-0.13130.33130.02420.04920.492-0.05220.613742.93536.101344.7573
33.2626-0.41390.83921.5627-0.40211.0325-0.09980.45910.2066-0.0483-0.0627-0.5486-0.05120.28650.1270.30120.01180.02110.31760.07710.350536.225717.803843.5043
43.548-0.02640.19092.9541.35161.7418-0.02580.0558-0.52530.4207-0.0945-0.01420.44030.07790.08190.2093-0.02510.01830.23910.04690.295111.608514.425242.0317
51.6728-0.35990.42452.90520.17129.31490.1621-0.06710.1087-0.0299-0.24150.6407-0.3773-0.3612-0.00250.175-0.09890.08130.27840.08660.51072.281723.788145.4342
61.6369-0.5677-0.96384.011-0.16823.20530.00410.1702-0.1788-0.1615-0.2226-0.2079-0.2051-0.02330.23190.3148-0.0541-0.00960.21120.09480.608217.928949.629843.2242
72.3034-0.1157-0.52593.40020.35292.0978-0.21340.2402-0.27450.60550.0223-0.4998-0.1384-0.06120.13340.3498-0.1156-0.09720.26340.14490.399716.222345.702755.2717
82.5871-1.78721.7973.014-1.09412.82610.32440.3214-0.10460.1649-0.5111-0.9003-0.60540.49770.26370.363-0.1216-0.04680.38550.10490.371817.433171.029536.166
92.05270.2880.44822.3434-0.22912.24470.12040.05390.24790.5427-0.10790.2469-0.3907-0.06580.00090.37110.0452-0.03020.1647-0.01510.27153.333475.185243.9856
103.3876-3.55142.62257.0380.04894.9484-0.0858-0.7369-0.26620.97380.13490.471-0.5041-0.9468-0.04070.7059-0.0135-0.12280.42440.12590.55955.722669.420360.4751
118.12823.3909-3.82615.9042-0.98385.52370.3337-0.9973-0.2721.4453-0.25440.1038-0.23380.10810.15180.8280.1192-0.06970.37960.08360.39753.58781.28355.3684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -2:49)
2X-RAY DIFFRACTION2chain 'A' and (resseq 50:84)
3X-RAY DIFFRACTION3chain 'A' and (resseq 85:183)
4X-RAY DIFFRACTION4chain 'A' and (resseq 184:313)
5X-RAY DIFFRACTION5chain 'A' and (resseq 314:345)
6X-RAY DIFFRACTION6chain 'B' and (resseq -1:84)
7X-RAY DIFFRACTION7chain 'B' and (resseq 85:147)
8X-RAY DIFFRACTION8chain 'B' and (resseq 148:183)
9X-RAY DIFFRACTION9chain 'B' and (resseq 184:292)
10X-RAY DIFFRACTION10chain 'B' and (resseq 293:319)
11X-RAY DIFFRACTION11chain 'B' and (resseq 320:345)

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