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- PDB-2q1w: Crystal structure of the Bordetella bronchiseptica enzyme WbmH in... -

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Basic information

Entry
Database: PDB / ID: 2q1w
TitleCrystal structure of the Bordetella bronchiseptica enzyme WbmH in complex with NAD+
ComponentsPutative nucleotide sugar epimerase/ dehydratase
KeywordsSUGAR BINDING PROTEIN / ROSSMANN FOLD / PROTEIN-NAD 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 / Putative nucleotide sugar epimerase/ dehydratase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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_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_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
C: Putative nucleotide sugar epimerase/ dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9026
Polymers109,9123
Non-polymers1,9903
Water7,476415
1
B: Putative nucleotide sugar epimerase/ dehydratase
C: Putative nucleotide sugar epimerase/ dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6014
Polymers73,2742
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-35 kcal/mol
Surface area23230 Å2
MethodPISA, PQS
2
A: Putative nucleotide sugar epimerase/ dehydratase
hetero molecules

A: Putative nucleotide sugar epimerase/ dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6014
Polymers73,2742
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.673, 158.988, 68.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a dimer. The asymmetric unit contains one complete dimer, formed by chains B and C. A second dimer is formed by chain A, together with a second molecule that is related by rotation around the two-fold axis 0,0,z.

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Components

#1: Protein Putative nucleotide sugar epimerase/ dehydratase


Mass: 36637.246 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BbLPS1.14, wbmH / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O87987
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 10 % (v/v) isopropanol, 20 % (w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.934
SYNCHROTRONSRS PX14.121.488
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 4, 2004
ADSC QUANTUM 42CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 channelSINGLE WAVELENGTHMx-ray1
2Si 111 channelSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
21.4881
ReflectionResolution: 2.19→30 Å / Num. all: 53222 / Num. obs: 49975 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.22 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.63 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PZK

2pzk


Resolution: 2.19→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.096 / SU ML: 0.132 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.5 / ESU R: 0.257 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22679 2559 5.1 %RANDOM
Rwork0.17609 ---
all0.179 53222 --
obs0.17866 47385 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.19→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6812 0 132 415 7359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227115
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9729716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63223.696322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.418151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.141545
X-RAY DIFFRACTIONr_chiral_restr0.1020.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025506
X-RAY DIFFRACTIONr_nbd_refined0.1950.23264
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24892
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2461
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.216
X-RAY DIFFRACTIONr_mcbond_it0.8741.54557
X-RAY DIFFRACTIONr_mcangle_it1.33127143
X-RAY DIFFRACTIONr_scbond_it2.0832872
X-RAY DIFFRACTIONr_scangle_it3.0054.52573
LS refinement shellResolution: 2.185→2.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 162 -
Rwork0.201 3029 -
obs--82.22 %

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