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- PDB-4evw: Crystal Structure of the nucleoside-diphosphate-sugar pyrophospho... -

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Basic information

Entry
Database: PDB / ID: 4evw
TitleCrystal Structure of the nucleoside-diphosphate-sugar pyrophosphorylase from Vibrio cholerae RC9. Northeast Structural Genomics Consortium (NESG) Target VcR193.
ComponentsNucleoside-diphosphate-sugar pyrophosphorylase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B gamma/epsilon subunits (EIF-2Bgamma/eIF-2Bepsilon)
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Alpha-Beta Complex / Alpha Beta / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsVorobiev, S. / Neely, H. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Kohan, E. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Neely, H. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Kohan, E. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the nucleoside-diphosphate-sugar pyrophosphorylase from Vibrio cholerae RC9.
Authors: Vorobiev, S. / Neely, H. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Kohan, E. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside-diphosphate-sugar pyrophosphorylase
B: Nucleoside-diphosphate-sugar pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2084
Polymers59,1592
Non-polymers492
Water6,954386
1
A: Nucleoside-diphosphate-sugar pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6042
Polymers29,5801
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoside-diphosphate-sugar pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6042
Polymers29,5801
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.303, 117.003, 128.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoside-diphosphate-sugar pyrophosphorylase


Mass: 29579.525 Da / Num. of mol.: 2 / Mutation: L211E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: RC9 / Gene: VCC_000301 / Plasmid: pET21_NESG, VcR193-L211E-21.6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: C2IC25
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 20% PEG 8000, 0.1M magnesium nitrate, 0.1M HEPES, pH 7.5, Microbatch crystallization under oil , temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 18, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 111486 / Num. obs: 111375 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 26.49 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 25.44
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3.16 / Num. unique all: 11100 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.247 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.24 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5653 5.09 %RANDOM
Rwork0.184 ---
obs0.185 111069 99.21 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.669 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 110.54 Å2 / Biso mean: 32.746 Å2 / Biso min: 13 Å2
Baniso -1Baniso -2Baniso -3
1--3.598 Å20 Å20 Å2
2--3.088 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 2 386 4348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084111
X-RAY DIFFRACTIONf_angle_d1.3345581
X-RAY DIFFRACTIONf_chiral_restr0.099586
X-RAY DIFFRACTIONf_plane_restr0.007730
X-RAY DIFFRACTIONf_dihedral_angle_d15.1371489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.894-1.9160.2611600.243038319885
1.916-1.9380.2441830.21935553738100
1.938-1.9620.2231530.22335213674100
1.962-1.9870.2171820.20135673749100
1.987-2.0130.2151660.19136133779100
2.013-2.040.2051980.19634853683100
2.04-2.0690.2221990.18835153714100
2.069-2.10.2171980.18935803778100
2.1-2.1330.1852020.18534673669100
2.133-2.1680.2081950.17635923787100
2.168-2.2060.2061960.18335463742100
2.206-2.2460.2521820.18234723654100
2.246-2.2890.232050.18435743779100
2.289-2.3360.1941690.17835383707100
2.336-2.3860.2072180.18235223740100
2.386-2.4420.1981740.1935433717100
2.442-2.5030.2022220.19834673689100
2.503-2.5710.2292040.2013511371599
2.571-2.6460.2012130.19535163729100
2.646-2.7320.2311900.1935543744100
2.732-2.8290.2552190.1973484370399
2.829-2.9420.2311800.20335263706100
2.942-3.0760.2021810.1993519370099
3.076-3.2380.1931760.1835763752100
3.238-3.4410.2131910.17535543745100
3.441-3.7070.1621900.16535403730100
3.707-4.0790.1711920.15635173709100
4.079-4.6680.1791600.1533528368899
4.668-5.8780.1911740.1835483722100
5.878-37.2550.2091810.2143448362997
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)
11.39690.2026-0.06691.420.24561.23340.02590.1129-0.044-0.1837-0.0123-0.0527-0.06220.0264-0.0120.1490.00350.00210.1325-0.010.129217.879870.243546.3823
21.44430.1409-0.06651.4461-0.40921.2950.03440.11010.0494-0.1754-0.019-0.00430.0440.0133-0.01640.15560.00440.00660.13210.0160.12286.2529108.423646.5529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 244
2X-RAY DIFFRACTION2chain BB1 - 244

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