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- PDB-5u4q: 1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimer... -

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Basic information

Entry
Database: PDB / ID: 5u4q
Title1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella pneumoniae in Complex with NAD.
ComponentsdTDP-glucose 4,6-dehydratase
KeywordsLIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NAD-Dependent Epimerase / Lipid-Binding Protein
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella pneumoniae in Complex with NAD.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.pdbx_keywords

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dTDP-glucose 4,6-dehydratase
B: dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3735
Polymers77,0112
Non-polymers1,3623
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-56 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.239, 55.845, 97.318
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein dTDP-glucose 4,6-dehydratase


Mass: 38505.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: rffG_4, rffG_2, SAMEA2273684_00396, SAMEA2273712_05182
Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: A0A169YGX7, dTDP-glucose 4,6-dehydratase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 7.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: PEGs II (E10), 0.2M Ammonium sulfate, 20% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2015 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 102114 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 24.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.588 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 5033 4.9 %RANDOM
Rwork0.1804 ---
obs0.18189 97040 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.325 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.49 Å2
2--0.78 Å20 Å2
3----1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.5→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4953 0 89 583 5625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195458
X-RAY DIFFRACTIONr_bond_other_d0.0010.024880
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9847450
X-RAY DIFFRACTIONr_angle_other_deg0.873311320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8175672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.56823.9259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.04115797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.291530
X-RAY DIFFRACTIONr_chiral_restr0.0860.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0216186
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021190
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_it1.9912.5672634
X-RAY DIFFRACTIONr_mcbond_other1.9792.5652633
X-RAY DIFFRACTIONr_mcangle_it3.0273.8253324
X-RAY DIFFRACTIONr_mcangle_other3.0273.8273325
X-RAY DIFFRACTIONr_scbond_it2.5092.8262824
X-RAY DIFFRACTIONr_scbond_other2.5092.8262825
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8274.1314127
X-RAY DIFFRACTIONr_long_range_B_refined5.74431.6416435
X-RAY DIFFRACTIONr_long_range_B_other5.65131.1866301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.504→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 328 -
Rwork0.266 6818 -
obs--94.72 %

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