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- PDB-3oa0: Crystal structure of the WlbA (WbpB) Dehydrogenase from Thermus t... -

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Basic information

Entry
Database: PDB / ID: 3oa0
TitleCrystal structure of the WlbA (WbpB) Dehydrogenase from Thermus thermophilus in complex with NAD and UDP-GlcNAcA
ComponentsLipopolysaccharide biosynthesis protein wbpB
KeywordsOXIDOREDUCTASE / sugar biosynthesis / dehydrogenase
Function / homology
Function and homology information


: / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...: / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HP7 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Lipopolysaccaride biosynthesis protein wbpB
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHolden, H.M. / Thoden, J.B.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and Functional Studies of WlbA: A Dehydrogenase Involved in the Biosynthesis of 2,3-Diacetamido-2,3-dideoxy-d-mannuronic Acid .
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Assembly

Deposited unit
A: Lipopolysaccharide biosynthesis protein wbpB
B: Lipopolysaccharide biosynthesis protein wbpB
C: Lipopolysaccharide biosynthesis protein wbpB
D: Lipopolysaccharide biosynthesis protein wbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,60816
Polymers139,3274
Non-polymers5,28112
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-95 kcal/mol
Surface area45860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.097, 68.320, 164.122
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lipopolysaccharide biosynthesis protein wbpB


Mass: 34831.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C0287, wbpB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q72KX8
#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-HP7 / (2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4-dihydroxy-oxane-2-carboxylic acid


Mass: 621.337 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H25N3O18P2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 298 K / pH: 7
Details: 15-20% PEG-5000, 100 mM MOPS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 14, 2009 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 98909 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 62.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 17.8 / Rsym value: 0.127 / % possible all: 85.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0066refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O9Z

3o9z


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.141 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4966 5 %RANDOM
Rwork0.189 ---
obs0.192 98901 91.8 %-
all-98901 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.97 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å20.06 Å2
2---0.86 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9781 0 340 442 10563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210429
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4782.01414250
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87651242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08622.296466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.082151665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.38415102
X-RAY DIFFRACTIONr_chiral_restr0.1520.21570
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217895
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3151.51552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.20122490
X-RAY DIFFRACTIONr_scbond_it3.34531003
X-RAY DIFFRACTIONr_scangle_it5.3614.5978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 361 -
Rwork0.226 6280 -
obs--84.33 %

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