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- PDB-5bjx: X-ray structure of the PglF 4,6-dehydratase from campylobacter je... -

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Basic information

Entry
Database: PDB / ID: 5bjx
TitleX-ray structure of the PglF 4,6-dehydratase from campylobacter jejuni, variant T395V, in complex with UDP
ComponentsWlaL protein
KeywordsMEMBRANE PROTEIN / short chain dehydrogenase / 4 / 6-dehydratase / deoxysugar / glycosylation
Function / homology
Function and homology information


UDP-N-acetylglucosamine 4,6-dehydratase (configuration-retaining) / lyase activity / nucleotide binding / membrane
Similarity search - Function
: / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 4,6-dehydratase (Configuration-retaining)
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRiegert, A.S. / 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: Biochemistry / Year: 2017
Title: Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily.
Authors: Riegert, A.S. / Thoden, J.B. / Schoenhofen, I.C. / Watson, D.C. / Young, N.M. / Tipton, P.A. / Holden, H.M.
History
DepositionSep 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WlaL protein
B: WlaL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,32419
Polymers81,6952
Non-polymers2,62917
Water13,151730
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-75 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.229, 108.251, 108.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein WlaL protein


Mass: 40847.449 Da / Num. of mol.: 2 / Fragment: UNP residues 244-590 / Mutation: T395V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaL / Production host: Escherichia coli (E. coli) / References: UniProt: O86159

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Non-polymers , 5 types, 747 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 22% PEG-5000, 2% MPD, 10 mM UDP, 100 mM MES

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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 210r / Detector: CCD / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 106859 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 58.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 21.2 / Num. unique obs: 10499 / Rsym value: 0.121 / % possible all: 98.4

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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: 5BJU

5bju


Resolution: 1.6→31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.184 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18483 5315 5 %RANDOM
Rwork0.16161 ---
obs0.16277 101508 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.776 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--1.19 Å20 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.6→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5309 0 166 730 6205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195656
X-RAY DIFFRACTIONr_bond_other_d0.0010.025681
X-RAY DIFFRACTIONr_angle_refined_deg1.7332.0257671
X-RAY DIFFRACTIONr_angle_other_deg0.797313170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1935710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.91526.233223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.336151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8471515
X-RAY DIFFRACTIONr_chiral_restr0.1080.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021116
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_it2.021.3322750
X-RAY DIFFRACTIONr_mcbond_other2.0111.3312749
X-RAY DIFFRACTIONr_mcangle_it2.6761.9933442
X-RAY DIFFRACTIONr_mcangle_other2.6771.9943443
X-RAY DIFFRACTIONr_scbond_it3.4851.6942906
X-RAY DIFFRACTIONr_scbond_other3.4851.6942906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3032.3674214
X-RAY DIFFRACTIONr_long_range_B_refined6.93412.647055
X-RAY DIFFRACTIONr_long_range_B_other6.93412.6437056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 386 -
Rwork0.166 7274 -
obs--96.83 %

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