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

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Basic information

Entry
Database: PDB / ID: 2pzm
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


glutamine metabolic process / 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 / MOLECULAR REPLACEMENT / Resolution: 2 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 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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

Downloads & links

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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)72,9999
Polymers70,5762
Non-polymers2,4237
Water8,521473
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.214, 140.481, 184.139
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-834-

HOH

DetailsThe biological unit is a dimer, made up of 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 1.6 M (NH4)2SO4, 2 % (v/v) PEG 400, 10 mM UDP, pH 7.5, 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: 2→30 Å / Num. all: 51224 / Num. obs: 51158 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.28 / % possible all: 100

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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
Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.963 / SU B: 5.135 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTHERMAL WITH TLS / Cross valid method: THROUGHOUT / ESU R: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2591 -RANDOM
Rwork0.1708 ---
obs0.1708 51115 99.68 %-
all-51224 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.315 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å20 Å2
2---1.3 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4685 0 136 473 5294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9956897
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3055651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94423.968189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80515734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1881524
X-RAY DIFFRACTIONr_chiral_restr0.1110.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023789
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22370
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23452
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2415
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.751.53241
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17525135
X-RAY DIFFRACTIONr_scbond_it1.86732011
X-RAY DIFFRACTIONr_scangle_it2.6514.51750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.224 3666 -
Rfree-0 -
obs--97.89 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
111.0953.54642.77226.7813-24.479625.77930.8782-0.3910.31710.9674-0.5387-0.86350.8716-0.0361-0.33960.3186-0.1965-0.1001-0.1202-0.0263-0.0248-12.056934.0641-2.9728
20.76170.6750.2812.8939-1.89212.10050.08670.01450.09240.2445-0.07650.32710.2963-0.0011-0.01020.1426-0.12810.0509-0.0303-0.0255-0.002-15.565844.7435-14.465
31.40570.9736-0.35284.775-1.77330.65860.133-0.1180.05870.3197-0.09110.26890.2126-0.1838-0.04190.1353-0.14160.04510.0153-0.0302-0.0132-19.380346.5408-12.2438
47.88763.0061-6.185913.8993-6.6086.2679-0.28770.10230.2271-0.0350.28720.48750.1048-0.5560.0005-0.018-0.2010.04120.0555-0.03770.0624-26.776248.2686-18.3406
51.9838-0.84840.02233.1672-0.64931.86790.1184-0.21210.2790.3343-0.11450.64640.0521-0.1301-0.00390.035-0.13240.14980.0338-0.02970.0127-20.431255.5843-9.3534
69.4154-5.32551.281214.809-5.399113.5041-0.2074-0.79730.69730.82750.3945-0.07870.1535-0.4259-0.18710.1039-0.10340.07430.0924-0.0313-0.062-15.304752.8258-1.5728
70.58940.4141-0.26120.91340.03361.01580.1092-0.02390.12490.0452-0.0560.1140.20090.084-0.05310.0459-0.07450.0276-0.0023-0.01520.0027-7.177657.6095-19.7214
81.3407-1.14460.68861.9588-0.57650.93710.13860.04620.0438-0.07790.02320.04890.14630.1328-0.16180.0612-0.05570.03850.0068-0.04840.0354-1.478360.8898-24.676
910.6308-0.98290.47148.6578-7.79377.58290.1393-0.1913-0.09980.169-0.014-0.24290.064-0.1798-0.12530.1184-0.09690.0109-0.0031-0.0283-0.0440.238956.7486-9.5617
100.80730.1858-0.83530.0427-0.19220.8642-0.00710.22690.06940.07150.1086-0.08050.3447-0.1658-0.10150.1213-0.10490.0270.04990.0278-0.0211-11.450447.5249-28.9884
115.15876.3897-8.361910.7912-4.763424.43040.24860.35660.45130.06260.06210.42970.3579-2.2499-0.3108-0.0163-0.3306-0.05350.54090.1435-0.0946-23.714444.2536-44.9326
1228.710113.35385.394113.87289.397321.0162-0.503-1.04011.7218-0.47890.09241.48010.3506-2.68190.4106-0.0554-0.1231-0.01050.53710.10850.0122-19.527650.8918-48.4728
131.36420.0901-0.60030.2626-0.65073.8286-0.02680.1481-0.1916-0.04630.0047-0.0930.6231-0.00010.02210.1577-0.05550.0395-0.0721-0.027-0.0388-6.183243.3065-26.9812
144.83144.831-0.68127.6285-1.6483.2460.1876-0.6172-0.16640.0725-0.09-0.46270.72170.8652-0.09750.21520.1107-0.0583-0.00040.0104-0.12052.707143.4148-11.1693
152.36770.84441.94370.8820.46077.5337-0.00230.2194-0.2411-0.13670.1904-0.26490.6892-0.0157-0.18820.1435-0.05090.0351-0.005-0.0274-0.0905-4.447544.3682-37.2705
1625.281312.9987-8.514319.8723-21.588425.32640.65321.2599-0.22140.9354-0.90540.5651.1099-0.57280.25220.3106-0.22660.0220.143-0.087-0.2561-17.730736.8773-45.678
1715.457225.6929-9.57743.2228-11.993435.79641.34260.0230.86750.0142-0.88883.25010.965-0.4428-0.45380.2304-0.2749-0.1580.43450.03240.0929-18.588543.7934-55.8829
180.90030.86850.67040.91930.89599.7514-0.10360.03980.49280.1876-0.09860.0622-0.2309-0.54560.20220.0216-0.01910.0160.08580.0011-0.0302-6.392156.4287-44.3306
195.0746-3.3813-1.8319.0095-10.80822.0734-0.21150.3207-0.1946-0.0926-0.0806-0.5830.38820.90110.29210.10290.02790.0036-0.0408-0.0742-0.0114.639744.5243-27.4839
204.28190.8041-0.87181.8167-0.36472.4595-0.38980.38060.0154-0.02640.24950.07040.8559-0.29730.14030.2127-0.15840.0226-0.1268-0.0361-0.1279-15.138238.633-28.8222
219.5996-7.685220.696836.6996-22.988845.9717-1.54831.448-0.6416-2.1825-0.84361.9868-0.5315-0.84472.39180.2767-0.2192-0.1085-0.0473-0.00140.2013-1.6684103.7993-32.8211
220.45031.302-0.06833.8418-0.35860.3482-0.0233-0.07080.23660.0792-0.08020.2416-0.20920.13890.10360.0801-0.12280.0196-0.03650.00550.06810.565692.8613-20.5025
230.95351.9901-1.4035.9537-2.89166.0833-0.0082-0.01440.1732-0.0451-0.02410.2674-0.2469-0.00590.03230.061-0.09640.0355-0.0526-0.01160.0456-3.3994.4606-18.2313
243.7113-7.77552.263418.6006-7.50364.6816-0.4822-0.46250.40251.11060.2524-1.5559-0.5031-0.24110.22980.1258-0.1457-0.00440.0322-0.11120.0627-0.640689.1348-5.5509
252.1151.5742-0.29475.21261.21791.75420.0989-0.10820.08430.4591-0.02890.2773-0.1357-0.1554-0.06990.0924-0.10210.0553-0.0449-0.04060.0071-8.287891.2947-13.6356
266.9129-10.61122.046727.46879.780915.5423-0.47040.2307-0.39590.2398-0.20910.4717-0.1643-1.69180.6795-0.1176-0.07410.01580.0089-0.02650.1848-16.039586.1091-21.03
271.4363-1.28741.95563.8456-2.26632.7605-0.0885-0.14780.010.12680.23270.3686-0.1526-0.2323-0.14420.0294-0.09380.03310.02780.00390.057-4.564984.4477-18.9116
280.9664-0.2084-1.14732.04671.46733.1206-0.0592-0.02060.11350.2909-0.14560.25260.08930.0640.20480.0696-0.11870.0716-0.0084-0.02370.037-4.762571.0209-12.1266
290.6103-0.59760.32582.1276-0.01980.74960.02030.09160.0275-0.1374-0.0203-0.0333-0.09920.12060.00010.0127-0.11330.02410.0279-0.00470.02341.434876.4352-24.5706
300.41480.8671-0.34022.0145-0.10022.12630.017-0.0123-0.06320.04570.0034-0.0679-0.14240.2331-0.02040.0053-0.09910.05110.0633-0.03480.02785.019269.2543-22.0911
315.0374-6.48341.793125.9462-7.26326.42810.0510.17490.2047-0.5258-0.36680.16180.0783-0.20950.31580.0467-0.09760.00330.0022-0.00940.0181-5.802976.6227-31.4776
320.50270.8180.59191.3381.02031.1629-0.07140.0038-0.197-0.06920.0423-0.1482-0.1693-0.05230.02910.0552-0.12080.0150.0590.02220.061210.923583.4594-16.468
333.9252-4.46182.861737.66264.17873.7811-0.2505-0.7816-0.1751-0.07180.37460.5632-0.34210.0488-0.1240.0046-0.1352-0.13140.14260.0736-0.076121.196485.3393-1.1729
341.7362-0.63730.918110.63628.313110.7020.1389-0.0875-0.39161.2369-0.1695-0.58060.73870.16730.03060.0504-0.1948-0.12940.07190.1319-0.009723.921678.6189-2.6703
352.9725-2.40612.00788.3788-1.2261.5918-0.05950.00760.17430.2225-0.1563-0.6108-0.02520.16150.2158-0.0232-0.1796-0.02060.09240.01650.049117.057984.2797-19.4871
364.5630.15250.57165.47493.88062.9639-0.11160.380.2161-0.48150.063-0.14-0.36160.21580.04860.1055-0.14480.07340.03210.0589-0.07576.638186.0571-31.2755
371.8597-1.12530.52552.50570.98522.348-0.38710.3184-0.0808-0.0880.3468-0.6522-0.46190.88280.0403-0.1007-0.1876-0.05620.13420.09910.138425.669881.7329-13.5526
381.09030.8691.927310.19513.29053.73070.5045-0.4052-0.05941.2386-0.5529-0.78850.61270.03130.04830.0122-0.2091-0.13870.25050.09930.08725.636774.2451-4.137
395.89-6.46886.548810.6719-11.63916.62170.17720.5265-0.1965-0.6298-0.2951-0.54390.29991.00750.118-0.0374-0.1690.10920.0853-0.01670.018916.432977.0507-29.6539
402.32650.63190.18222.54041.49142.6416-0.00480.08850.35680.10760.0449-0.3043-0.43410.3672-0.04010.0021-0.1914-0.0292-0.00870.08030.033415.954592.4743-14.6231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 0
2X-RAY DIFFRACTION2A1 - 20
3X-RAY DIFFRACTION3A21 - 34
4X-RAY DIFFRACTION4A35 - 44
5X-RAY DIFFRACTION5A45 - 60
6X-RAY DIFFRACTION6A61 - 69
7X-RAY DIFFRACTION7A70 - 129
8X-RAY DIFFRACTION8A130 - 150
9X-RAY DIFFRACTION9A151 - 156
10X-RAY DIFFRACTION10A157 - 179
11X-RAY DIFFRACTION11A180 - 186
12X-RAY DIFFRACTION12A187 - 191
13X-RAY DIFFRACTION13A192 - 213
14X-RAY DIFFRACTION14A214 - 219
15X-RAY DIFFRACTION15A220 - 237
16X-RAY DIFFRACTION16A238 - 243
17X-RAY DIFFRACTION17A244 - 249
18X-RAY DIFFRACTION18A250 - 263
19X-RAY DIFFRACTION19A264 - 271
20X-RAY DIFFRACTION20A272 - 308
21X-RAY DIFFRACTION21B-6 - -1
22X-RAY DIFFRACTION22B0 - 20
23X-RAY DIFFRACTION23B21 - 33
24X-RAY DIFFRACTION24B34 - 39
25X-RAY DIFFRACTION25B40 - 59
26X-RAY DIFFRACTION26B60 - 64
27X-RAY DIFFRACTION27B65 - 82
28X-RAY DIFFRACTION28B83 - 94
29X-RAY DIFFRACTION29B95 - 127
30X-RAY DIFFRACTION30B128 - 150
31X-RAY DIFFRACTION31B151 - 156
32X-RAY DIFFRACTION32B157 - 178
33X-RAY DIFFRACTION33B179 - 182
34X-RAY DIFFRACTION34B183 - 195
35X-RAY DIFFRACTION35B196 - 203
36X-RAY DIFFRACTION36B204 - 222
37X-RAY DIFFRACTION37B223 - 241
38X-RAY DIFFRACTION38B242 - 260
39X-RAY DIFFRACTION39B261 - 273
40X-RAY DIFFRACTION40B274 - 306

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