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- PDB-2pzl: Crystal structure of the Bordetella bronchiseptica enzyme WbmG in... -

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Basic information

Entry
Database: PDB / ID: 2pzl
TitleCrystal structure of the Bordetella bronchiseptica enzyme WbmG in complex with NAD and UDP
ComponentsPutative nucleotide sugar epimerase/ dehydratase
KeywordsSUGAR BINDING PROTEIN / ROSSMANN FOLD / PROTEIN-NAD COMPLEX / PROTEIN-NUCLEOTIDE COMPLEX
Function / homology
Function and homology information


transferase activity / nucleotide binding
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / Putative nucleotide sugar epimerase/ dehydratase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single Wavelength / Resolution: 2.39 Å
AuthorsKing, J.D. / Harmer, N.J. / Maskell, D.J. / Blundell, T.L.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Predicting protein function from structure--the roles of short-chain dehydrogenase/reductase enzymes in Bordetella O-antigen biosynthesis.
Authors: King, J.D. / Harmer, N.J. / Preston, A. / Palmer, C.M. / Rejzek, M. / Field, R.A. / Blundell, T.L. / Maskell, D.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Cloning, expression, purification and preliminary crystallographic analysis of the short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica.
Authors: Harmer, N.J. / King, J.D. / Palmer, C.M. / Preston, A. / Maskell, D.J. / Blundell, T.L.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Aug 30, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Putative nucleotide sugar epimerase/ dehydratase
B: Putative nucleotide sugar epimerase/ dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7116
Polymers70,5762
Non-polymers2,1354
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.226, 49.792, 75.912
Angle α, β, γ (deg.)90.00, 101.12, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: -1 - 306 / Label seq-ID: 19 - 326

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a dimer, formed from chains A and B.

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Components

#1: Protein Putative nucleotide sugar epimerase/ dehydratase


Mass: 35287.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BbLPS1.15, wbmG / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O87988
#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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.2 M MgCl2, 16-18 % (w/w) PEG 8000. UDP-glucose was added by soaking at 10 mM prior to cryoprotection. pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2004
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. all: 27912 / Num. obs: 27549 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4 / Redundancy: 4.47 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 4.45 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.98 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: Single Wavelength
Starting model: RELATED PDB ENTRY 2PZK WAS SOLVED BY MAD, AND USED AS A STARTING MODEL.

2pzk


Resolution: 2.39→29.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.064 / SU ML: 0.189 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23541 1385 5 %RANDOM
Rwork0.18608 ---
all0.189 27912 --
obs0.18867 26162 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.634 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.13 Å2
2--0.18 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.39→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4669 0 130 154 4953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224925
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9976741
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39823.946185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12915738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0981523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023685
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.22141
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23329
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.218
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.53149
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27424994
X-RAY DIFFRACTIONr_scbond_it1.87131999
X-RAY DIFFRACTIONr_scangle_it2.7854.51745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1217medium positional0.120.5
1079loose positional0.35
1217medium thermal0.952
1079loose thermal1.6310
LS refinement shellResolution: 2.395→2.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 79 -
Rwork0.256 1848 -
obs--93.73 %

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