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- PDB-6bwl: X-ray structure of Pal from Bacillus thuringiensis -

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Basic information

Entry
Database: PDB / ID: 6bwl
TitleX-ray structure of Pal from Bacillus thuringiensis
ComponentsPal
KeywordsLYASE / short chain dehydrogenase / deoxysugar
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide binding
Similarity search - Function
GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / 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 / URIDINE-5'-DIPHOSPHATE / Pal
Similarity search - Component
Biological speciesBacillus thuringiensis serovar israelensis ATCC 35646 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 15, 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 ...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 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,14610
Polymers36,7361
Non-polymers1,4109
Water10,052558
1
A: Pal
hetero molecules

A: Pal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,29120
Polymers73,4722
Non-polymers2,82018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8540 Å2
ΔGint-86 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.420, 98.341, 98.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

21A-728-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pal / dTDP-glucose 4 / 6-dehydratase


Mass: 36735.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar israelensis ATCC 35646 (bacteria)
Gene: RBTH_04254 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ESA4, dTDP-glucose 4,6-dehydratase

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Non-polymers , 6 types, 567 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8-12% PEG 5000, 100 mM MES, 2% MPD, 5 mM UDP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 82030 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 53.7
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 8 / Num. unique obs: 8031 / Rsym value: 0.175 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p5u

2p5u


Resolution: 1.45→23.5 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.695 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.045 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15115 3981 4.9 %RANDOM
Rwork0.12946 ---
obs0.13053 78049 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2---1.1 Å20 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.45→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 88 558 3094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192627
X-RAY DIFFRACTIONr_bond_other_d0.0010.022501
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9873579
X-RAY DIFFRACTIONr_angle_other_deg0.80835774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51726.121116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25315452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.473155
X-RAY DIFFRACTIONr_chiral_restr0.1060.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
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_it1.3071.1331267
X-RAY DIFFRACTIONr_mcbond_other1.2951.131266
X-RAY DIFFRACTIONr_mcangle_it1.8511.6961586
X-RAY DIFFRACTIONr_mcangle_other1.8531.6991587
X-RAY DIFFRACTIONr_scbond_it3.1011.3921360
X-RAY DIFFRACTIONr_scbond_other3.1011.3921360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4931.971986
X-RAY DIFFRACTIONr_long_range_B_refined6.59612.7843705
X-RAY DIFFRACTIONr_long_range_B_other6.59512.7883706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 297 -
Rwork0.185 5593 -
obs--97.29 %

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