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- PDB-6bwc: X-ray structure of Pen from Bacillus thuringiensis -

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Basic information

Entry
Database: PDB / ID: 6bwc
TitleX-ray structure of Pen from Bacillus thuringiensis
ComponentsPolysaccharide biosynthesis protein CapD
KeywordsBIOSYNTHETIC PROTEIN / shout chain dehydrogenase / flagellin glycosylation / deoxy-sugar
Function / homology
Function and homology information


Polysaccharide biosynthesis protein, CapD-like domain / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Polysaccharide biosynthesis protein CapD
Similarity search - Component
Biological speciesBacillus thuringiensis HD-771 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDelvaux, N.A. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Protein Sci. / Year: 2018
Title: Molecular architectures of Pen and Pal: Key enzymes required for CMP-pseudaminic acid biosynthesis in Bacillus thuringiensis.
Authors: Delvaux, N.A. / Thoden, J.B. / Holden, H.M.
History
DepositionDec 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polysaccharide biosynthesis protein CapD
B: Polysaccharide biosynthesis protein CapD
C: Polysaccharide biosynthesis protein CapD
D: Polysaccharide biosynthesis protein CapD
E: Polysaccharide biosynthesis protein CapD
F: Polysaccharide biosynthesis protein CapD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,23223
Polymers232,6486
Non-polymers8,58517
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33100 Å2
ΔGint-176 kcal/mol
Surface area70810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.524, 141.876, 93.244
Angle α, β, γ (deg.)90.00, 111.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Polysaccharide biosynthesis protein CapD


Mass: 38774.598 Da / Num. of mol.: 6 / Mutation: D128N, K129A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis HD-771 (bacteria)
Gene: BTG_02000 / Production host: Escherichia coli (E. coli) / References: UniProt: J3UJH9
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C17H27N3O17P2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.2-2.5 M ammonium sulfate, 100 mM HEPES, 5 mM UDP-GlcNAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→86.66 Å / Num. obs: 55673 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5327 / Rsym value: 0.301 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gn4

2gn4


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.856 / SU B: 16.183 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2896 5.2 %RANDOM
Rwork0.20133 ---
obs0.20395 52775 90.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.501 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å2-0.92 Å2
2--3.28 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15321 0 547 134 16002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916120
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215584
X-RAY DIFFRACTIONr_angle_refined_deg1.7332.00921771
X-RAY DIFFRACTIONr_angle_other_deg0.998335908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57251913
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51724.884692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.374152984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5441582
X-RAY DIFFRACTIONr_chiral_restr0.0850.22516
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217557
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023563
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_it1.3992.6017721
X-RAY DIFFRACTIONr_mcbond_other1.3992.6017720
X-RAY DIFFRACTIONr_mcangle_it2.3843.8919611
X-RAY DIFFRACTIONr_mcangle_other2.3843.8919612
X-RAY DIFFRACTIONr_scbond_it1.2832.698399
X-RAY DIFFRACTIONr_scbond_other1.2752.6828378
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2183.95512131
X-RAY DIFFRACTIONr_long_range_B_refined4.03319.50417186
X-RAY DIFFRACTIONr_long_range_B_other4.00819.50417180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 176 -
Rwork0.315 3633 -
obs--84.1 %

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