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- PDB-3pvz: UDP-N-acetylglucosamine 4,6-dehydratase from Vibrio fischeri -

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Basic information

Entry
Database: PDB / ID: 3pvz
TitleUDP-N-acetylglucosamine 4,6-dehydratase from Vibrio fischeri
ComponentsUDP-N-acetylglucosamine 4,6-dehydratase
KeywordsLYASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / lyase activity / nucleotide binding
Similarity search - Function
UDP-galactose 4-epimerase; domain 1 - #40 / : / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / 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 / THIOCYANATE ION / UDP-N-acetylglucosamine 4,6-dehydratase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsOsipiuk, J. / Marshall, N. / Tesar, C. / Pearson, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: UDP-N-acetylglucosamine 4,6-dehydratase from Vibrio fischeri.
Authors: Osipiuk, J. / Marshall, N. / Tesar, C. / Pearson, L. / Buck, K. / Joachimiak, A.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
SupersessionJan 26, 2011ID: 3NZO
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 4,6-dehydratase
B: UDP-N-acetylglucosamine 4,6-dehydratase
C: UDP-N-acetylglucosamine 4,6-dehydratase
D: UDP-N-acetylglucosamine 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,54616
Polymers184,5334
Non-polymers3,01312
Water6,431357
1
A: UDP-N-acetylglucosamine 4,6-dehydratase
B: UDP-N-acetylglucosamine 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7789
Polymers92,2662
Non-polymers1,5127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-34 kcal/mol
Surface area27790 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine 4,6-dehydratase
D: UDP-N-acetylglucosamine 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7677
Polymers92,2662
Non-polymers1,5015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-33 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.920, 74.837, 88.789
Angle α, β, γ (deg.)102.710, 95.150, 100.350
Int Tables number1
Space group name H-MP1
DetailsPUTATIVE BIOLOGICAL UNIT IS A DIMER, CHAINS A AND B

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Components

#1: Protein
UDP-N-acetylglucosamine 4,6-dehydratase


Mass: 46133.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: VF_0140 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5E8L1, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2 M sodium thiocyanate, 20 % PEG-3350, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→38.8 Å / Num. all: 97465 / Num. obs: 97465 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.088 / Χ2: 3.585 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.1-2.142.20.4431.8346720.97994.1
2.14-2.182.30.42148021.00396.2
2.18-2.222.30.36148151.04197.1
2.22-2.262.40.33349071.09797.3
2.26-2.312.40.30348141.09397.4
2.31-2.372.40.25348471.22497.5
2.37-2.422.40.24649281.26197.7
2.42-2.492.40.19348431.32597.7
2.49-2.562.40.18749101.49197.8
2.56-2.652.40.16248681.63898
2.65-2.742.40.14548371.83398
2.74-2.852.40.12549542.30698.3
2.85-2.982.40.10948932.62898.2
2.98-3.142.40.09848843.08798.3
3.14-3.332.40.08349233.6698.4
3.33-3.592.40.07449084.65598.7
3.59-3.952.40.06949215.68598.6
3.95-4.522.30.06549217.16898.7
4.52-5.72.30.06749339.7698.9
5.7-502.40.078488518.50897.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 12.3 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 4853 5 %RANDOM
Rwork0.1866 ---
all0.189 97460 --
obs0.189 97460 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.35 Å2 / Biso mean: 49.586 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å21.47 Å20.53 Å2
2--0.41 Å2-2.84 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11337 0 194 357 11888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02211973
X-RAY DIFFRACTIONr_bond_other_d0.0010.028255
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.97516175
X-RAY DIFFRACTIONr_angle_other_deg0.905320155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34751465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51624.875599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.213152209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.151569
X-RAY DIFFRACTIONr_chiral_restr0.0830.21782
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022466
X-RAY DIFFRACTIONr_mcbond_it0.7671.57130
X-RAY DIFFRACTIONr_mcbond_other0.1881.52893
X-RAY DIFFRACTIONr_mcangle_it1.39211532
X-RAY DIFFRACTIONr_scbond_it2.3134843
X-RAY DIFFRACTIONr_scangle_it3.4434.54610
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 332 -
Rwork0.285 6362 -
all-6694 -
obs-6694 90.63 %
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)
10.7458-0.3255-0.20150.39580.0350.9399-0.1393-0.27450.22080.11250.0877-0.0099-0.05550.0310.05160.16460.03870.00310.1535-0.05330.178714.317770.33498.6464
21.6204-0.37330.24440.87581.0032.2271-0.1634-0.5227-0.2090.31390.2177-0.03930.55810.0689-0.05430.24150.0590.00810.24130.08070.162839.434855.0475103.8787
31.1873-0.13280.15240.62340.29060.25840.06780.0701-0.32610.127-0.17290.1880.0508-0.1680.10510.1257-0.02-0.00090.1983-0.07870.2462-2.592828.592766.9735
40.7654-0.0026-0.19320.90340.57410.49580.03470.4646-0.0105-0.2705-0.0379-0.0098-0.1822-0.09870.00310.20710.04890.02470.31410.02090.041818.359442.576153.3883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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