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- PDB-3nkl: Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vib... -

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Basic information

Entry
Database: PDB / ID: 3nkl
TitleCrystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri
ComponentsUDP-D-quinovosamine 4-dehydrogenase
Keywordsoxidoreductase/lyase / alpha-beta fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / oxidoreductase-lyase complex
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / lyase activity / membrane
Similarity search - Function
CoA-binding domain / : / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / UDP-D-quinovosamine 4-dehydrogenase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKim, Y. / Mack, J. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2010
Title: Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri
Authors: Kim, Y. / Mack, J. / Buck, K. / Joachimiak, A.
History
DepositionJun 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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-D-quinovosamine 4-dehydrogenase
B: UDP-D-quinovosamine 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,28411
Polymers31,5242
Non-polymers7609
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-94 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.262, 45.379, 69.813
Angle α, β, γ (deg.)90.00, 91.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-D-quinovosamine 4-dehydrogenase


Mass: 15762.071 Da / Num. of mol.: 2 / Fragment: residues 144-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: VF_0197 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q5E8F4, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, Lyases; Carbon-oxygen lyases; Hydro-lyases

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Non-polymers , 5 types, 253 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25 %w/v Polyehtlyene glycol 3,350, 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: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 25582 / Num. obs: 25582 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 24.67 Å2 / Rsym value: 0.051 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.26 / Num. unique all: 832 / Rsym value: 0.341 / % possible all: 62.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.217 Å / SU ML: 0.24 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1281 5.03 %random
Rwork0.167 ---
all0.169 25491 --
obs0.169 25491 94.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.645 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1--6.3112 Å20 Å2-1.4354 Å2
2--5.0756 Å2-0 Å2
3---1.2356 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 42 244 2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092058
X-RAY DIFFRACTIONf_angle_d1.2162774
X-RAY DIFFRACTIONf_dihedral_angle_d16.23794
X-RAY DIFFRACTIONf_chiral_restr0.091326
X-RAY DIFFRACTIONf_plane_restr0.005343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8986-1.97460.25171020.20211878198066
1.9746-2.06450.21861160.17412486260288
2.0645-2.17340.19571520.15842818297098
2.1734-2.30950.18341520.14832768292099
2.3095-2.48780.19561530.16422822297599
2.4878-2.73810.22471270.18482824295199
2.7381-3.13420.25921380.175428572995100
3.1342-3.94830.16841560.160528743030100
3.9483-42.22740.1611850.14882883306899
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)
13.32080.2217-0.21411.90350.17222.75460.02250.56380.1003-0.223-0.08230.0471-0.0079-0.10430.06830.16280.07330.00480.26330.00580.10421.590612.420917.5411
23.4071-2.00410.48922.96150.11.42160.10860.3592-0.03260.0087-0.1432-0.11180.0512-0.01120.03580.00350.00430.00540.0413-0.00630.085922.36272.778925.3528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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