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- PDB-2q1s: Crystal structure of the Bordetella bronchiseptica enzyme WbmF in... -

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Basic information

Entry
Database: PDB / ID: 2q1s
TitleCrystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NADH
ComponentsPutative nucleotide sugar epimerase/ dehydratase
KeywordsSUGAR BINDING PROTEIN / ROSSMANN FOLD / PROTEIN-NADH COMPLEX
Function / homology
Function and homology information


transferase activity / nucleotide binding
Similarity search - Function
UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Putative nucleotide sugar epimerase/ dehydratase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHarmer, N.J. / King, J.D. / Palmer, C.M. / Maskell, D. / 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: Advisory / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2602
Polymers41,5951
Non-polymers6651
Water4,468248
1
A: Putative nucleotide sugar epimerase/ dehydratase
hetero molecules

A: Putative nucleotide sugar epimerase/ dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5214
Polymers83,1902
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5270 Å2
ΔGint-44 kcal/mol
Surface area25960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.186, 77.875, 59.411
Angle α, β, γ (deg.)90.00, 108.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

DetailsThe biological assembly is a dimer. The second part of the biological assembly is generated by rotation around the two fold axis 0, y, 0, followed by a translation of 0, 0, 1.

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Components

#1: Protein Putative nucleotide sugar epimerase/ dehydratase


Mass: 41594.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BbLPS1.16, wbmF / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O87989
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M bicine, 16 % (w/w) PEG 8000, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2006
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 57672 / Num. obs: 57271 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.8 / Redundancy: 4.8 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.83 / Num. unique all: 2698 / % possible all: 94.8

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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 ENTRIES 1BXK, 1KEU, 1R6D

1bxk

1keu

1r6d


Resolution: 1.5→38.52 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.087 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22622 2854 5 %RANDOM
Rwork0.19185 ---
all0.194 57672 --
obs0.19358 54327 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.6 Å2
2--1.2 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 44 248 2856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222705
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9663695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1845345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38224.188117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31315423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9141514
X-RAY DIFFRACTIONr_chiral_restr0.1110.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022051
X-RAY DIFFRACTIONr_nbd_refined0.2060.21268
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.211
X-RAY DIFFRACTIONr_mcbond_it0.9891.51711
X-RAY DIFFRACTIONr_mcangle_it1.58822709
X-RAY DIFFRACTIONr_scbond_it2.02631118
X-RAY DIFFRACTIONr_scangle_it2.864.5980
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 238 -
Rwork0.363 3866 -
obs--96.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.3054-2.6870.603320.93379.08564.2577-0.34290.4257-0.7637-0.7876-0.05250.37480.50370.68860.39540.0219-0.0752-0.01410.03990.1016-0.150630.777917.3519-4.8948
23.4102-0.4233-1.40241.40240.39395.4022-0.0850.5301-0.069-0.35950.02790.05370.3525-0.33370.0571-0.0818-0.1535-0.0152-0.1759-0.0025-0.242922.731713.02752.7559
34.7850.34591.5281.4183-0.60190.85220.09730.4904-0.3936-0.2743-0.1169-0.00880.1999-0.54990.0196-0.0126-0.1385-0.024-0.2339-0.0413-0.102720.57715.24710.404
43.5217-0.1768-0.37020.9103-0.32630.8735-0.02550.0333-0.2145-0.1370.04290.03820.28290.0254-0.0174-0.0505-0.06310.0273-0.23680.002-0.154827.71648.367715.3898
53.2698-0.465-0.47091.28970.35874.156-0.190.06250.0708-0.10310.07150.0694-0.01680.20370.1185-0.096-0.09790.0414-0.17120.0017-0.222834.847718.803110.3634
60.24390.42150.95754.00922.4693.96190.24190.19840.48280.15880.14070.5771-0.7773-0.5341-0.38260.00990.0405-0.023-0.09610.0251-0.060528.210429.616228.5829
72.77630.1667-0.67851.2949-0.34733.4594-0.1201-0.07370.2275-0.07820.09140.00690.02740.05310.0287-0.1218-0.03980.0166-0.2120.0062-0.206632.389820.979919.5039
82.4384-0.29090.75851.743-0.45791.696-0.0126-0.194-0.0381-0.1799-0.04330.31560.1398-0.29920.056-0.2749-0.1222-0.0405-0.0920.0172-0.18767.081214.444117.9697
910.6112.34441.77587.839611.644817.59080.3997-0.4823-0.392.70050.1120.89221.4825-0.6643-0.5117-0.1387-0.257-0.0511-0.01970.0567-0.0221-5.838218.752818.9336
1019.5739-3.9706-10.76312.27235.868715.1774-0.7632-1.7587-0.04-0.0145-0.15080.29340.93090.50390.914-0.281-0.01790.0541-0.13-0.119-0.07434.079130.32723.7217
116.3993-1.69111.95817.60835.24479.2695-0.22140.23820.2866-0.19270.14420.27920.1701-0.17020.0772-0.2244-0.0583-0.076-0.13880.086-0.144312.988325.13729.2215
124.8603-0.14450.75970.66520.07581.348-0.07490.44850.2523-0.23270.10740.014-0.1196-0.1471-0.0325-0.1086-0.0731-0.0249-0.1860.0875-0.190126.458526.21677.2297
131.1222-2.671.24726.3528-2.96761.3862-0.2558-0.11330.71460.23920.02950.3727-0.081-0.26830.22630.0407-0.0218-0.0240.08760.02550.10637.380333.241916.1371
148.4409-3.4987-6.12581.85371.57196.76380.38840.08030.00340.4636-0.23280.4209-0.2007-0.7371-0.1557-0.414-0.038-0.1012-0.14190.1058-0.027-2.944226.67312.2225
1520.5332.9533-0.431913.80885.45712.2851-0.03261.1691.1243-0.26190.03361.6567-0.89780.2944-0.0010.0313-0.0834-0.03010.07290.05330.0772-7.97927.999219.4213
161.89470.6255-0.57574.08982.10731.5341-0.60781.7930.0515-0.58720.50750.07220.1917-0.07810.1004-0.01520.13390.0337-0.1678-0.06630.05394.212639.098926.7874
177.1474-1.9739-8.14112.61563.609110.1674-0.1736-0.6490.70080.5896-0.18080.9368-0.0812-1.38480.35440.02560.0099-0.1513-0.11980.12780.063121.376635.477813.4605
1814.26993.1592-0.82313.18530.6763.3904-0.15481.51980.5557-0.14630.18320.3338-0.4573-0.4236-0.0284-0.058-0.0138-0.1159-0.22010.197-0.188816.224330.52114.5935
193.4861-0.4253-1.35881.06021.8493.33970.08770.1966-0.2451-0.241-0.01650.57170.1869-0.5008-0.0712-0.1908-0.1661-0.0913-0.0178-0.025-0.01072.734410.079311.5764
2023.651510.39185.044312.132919.319639.733-1.3339-0.84920.0072.38960.08750.48260.2197-1.54781.2465-0.0746-0.14010.18890.00770.1407-0.09114.28496.458631.5397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 1229 - 32
2X-RAY DIFFRACTION2AA13 - 3833 - 58
3X-RAY DIFFRACTION3AA39 - 5259 - 72
4X-RAY DIFFRACTION4AA53 - 11773 - 137
5X-RAY DIFFRACTION5AA118 - 148138 - 168
6X-RAY DIFFRACTION6AA149 - 157169 - 177
7X-RAY DIFFRACTION7AA158 - 189178 - 209
8X-RAY DIFFRACTION8AA190 - 223210 - 243
9X-RAY DIFFRACTION9AA224 - 229244 - 249
10X-RAY DIFFRACTION10AA230 - 238250 - 258
11X-RAY DIFFRACTION11AA239 - 244259 - 264
12X-RAY DIFFRACTION12AA245 - 268265 - 288
13X-RAY DIFFRACTION13AA269 - 273289 - 293
14X-RAY DIFFRACTION14AA274 - 286294 - 306
15X-RAY DIFFRACTION15AA287 - 292307 - 312
16X-RAY DIFFRACTION16AA293 - 300313 - 320
17X-RAY DIFFRACTION17AA301 - 312321 - 332
18X-RAY DIFFRACTION18AA313 - 327333 - 347
19X-RAY DIFFRACTION19AA328 - 350348 - 370
20X-RAY DIFFRACTION20AA351 - 356371 - 376

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