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- PDB-2y0d: BceC mutation Y10K -

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Basic information

Entry
Database: PDB / ID: 2y0d
TitleBceC mutation Y10K
ComponentsUDP-GLUCOSE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CARBOHYDRATE SYNTHESIS / EXOPOLYSACCHARIDE / CYSTIC FIBROSIS
Function / homology
Function and homology information


UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / polysaccharide biosynthetic process / NAD binding
Similarity search - Function
UDP-glucose 6-dehydrogenase, bacterial type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-glucose 6-dehydrogenase, bacterial type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / Cytochrome c1, transmembrane anchor, C-terminal / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesBURKHOLDERIA CEPACIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRocha, J. / Popescu, A.O. / Borges, P. / Mil-Homens, D. / Sa-Correia, I. / Fialho, A.M. / Frazao, C.
Citation
Journal: J.Bacteriol. / Year: 2011
Title: Structure of Burkholderia Cepacia Udp-Glucose Dehydrogenase (Ugd) Bcec and Role of Tyr10 in Final Hydrolysis of Ugd Thioester Intermediate.
Authors: Rocha, J. / Popescu, A.O. / Borges, P. / Mil-Homens, D. / Moreira, L.M. / Sa-Correia, I. / Fialho, A.M. / Frazao, C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Cloning, Expression, Purification, Crystallization and Preliminary Crystallographic Studies of Bcec, a Udp-Glucose Dehydrogenase from Burkholderia Cepacia Ist408.
Authors: Rocha, J. / Popescu, A.O. / Sa-Correia, I. / Fialho, A.M. / Frazao, C.
History
DepositionDec 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: UDP-GLUCOSE DEHYDROGENASE
B: UDP-GLUCOSE DEHYDROGENASE
C: UDP-GLUCOSE DEHYDROGENASE
D: UDP-GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,13816
Polymers209,0484
Non-polymers3,09012
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20260 Å2
ΔGint-226.2 kcal/mol
Surface area65440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.622, 109.250, 183.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 0:87 OR RESSEQ 93:143 OR RESSEQ 145:453 )
211CHAIN B AND (RESSEQ 0:87 OR RESSEQ 93:143 OR RESSEQ 145:453 )
311CHAIN C AND (RESSEQ 0:87 OR RESSEQ 93:143 OR RESSEQ 145:453 )
411CHAIN D AND (RESSEQ 0:87 OR RESSEQ 93:143 OR RESSEQ 145:453 )

NCS oper:
IDCodeMatrixVector
1given(-0.01687, 0.9937, 0.1107), (0.9963, 0.007397, 0.08547), (0.08412, 0.1117, -0.9902)72.15, -74.69, 35.41
2given(-0.06221, -0.9112, 0.4073), (-0.9107, -0.1151, -0.3967), (0.4084, -0.3956, -0.8227)4.28, 83.04, 13.07
3given(-0.869, -0.107, -0.4831), (-0.06793, -0.9413, 0.3307), (-0.4901, 0.3202, 0.8107)154.9, 4.082, 35.89

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Components

#1: Protein
UDP-GLUCOSE DEHYDROGENASE / BCEC


Mass: 52261.988 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA CEPACIA (bacteria) / Strain: IST 408 / Plasmid: PBCEC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SURE / References: UniProt: C9E261, UDP-glucose 6-dehydrogenase
#2: Chemical
ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID / Uridine diphosphate glucuronic acid


Mass: 580.285 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N2O18P2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 10 TO LYS ENGINEERED RESIDUE IN CHAIN B, TYR 10 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, TYR 10 TO LYS ENGINEERED RESIDUE IN CHAIN B, TYR 10 TO LYS ENGINEERED RESIDUE IN CHAIN C, TYR 10 TO LYS ENGINEERED RESIDUE IN CHAIN D, TYR 10 TO LYS

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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: 2.44 Å3/Da / Density % sol: 48.9 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: AT 293 K UPON VAPOR DIFFUSION OF SITTING DROPS OF 1 MICRO-LITER PROTEIN SOLUTION (5 MG/ML PROTEIN, 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT, 0.25 MM UDP-GLCA, AND 0.5 MM OXIDIZED NAD), ...Details: AT 293 K UPON VAPOR DIFFUSION OF SITTING DROPS OF 1 MICRO-LITER PROTEIN SOLUTION (5 MG/ML PROTEIN, 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT, 0.25 MM UDP-GLCA, AND 0.5 MM OXIDIZED NAD), AND 1 MICRO-LITER WELL SOLUTION (200 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE PH 4.5, 11-14 % (W/V) PEG 4K, AND 50 MM NAF), EQUILIBRATED AGAINST 500 MICRO-LITER PRECIPITATION SOLUTION IN THE WELL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.8→57.83 Å / Num. obs: 50832 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 27.74 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 2.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE BCEC WITH TYR 10 TRUNCATED TO ALA

Resolution: 2.8→54.63 Å / SU ML: 1.02 / σ(F): 1.36 / Phase error: 16.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 2576 5.1 %
Rwork0.212 --
obs0.21 50791 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.37 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.8056 Å20 Å20 Å2
2---7.5775 Å20 Å2
3---0.9821 Å2
Refinement stepCycle: LAST / Resolution: 2.8→54.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13937 0 188 0 14125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01314387
X-RAY DIFFRACTIONf_angle_d1.41619503
X-RAY DIFFRACTIONf_dihedral_angle_d17.9015287
X-RAY DIFFRACTIONf_chiral_restr0.0982166
X-RAY DIFFRACTIONf_plane_restr0.0062558
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3455X-RAY DIFFRACTIONPOSITIONAL
12B3455X-RAY DIFFRACTIONPOSITIONAL0.083
13C3455X-RAY DIFFRACTIONPOSITIONAL0.099
14D3455X-RAY DIFFRACTIONPOSITIONAL0.091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.85390.3281320.24942625X-RAY DIFFRACTION100
2.8539-2.91210.30331350.24392690X-RAY DIFFRACTION100
2.9121-2.97540.30031560.24992626X-RAY DIFFRACTION100
2.9754-3.04460.3041520.24562644X-RAY DIFFRACTION100
3.0446-3.12080.30941420.25892667X-RAY DIFFRACTION100
3.1208-3.20510.31151460.25112643X-RAY DIFFRACTION100
3.2051-3.29940.32111430.22922656X-RAY DIFFRACTION100
3.2994-3.40590.26911520.23222657X-RAY DIFFRACTION100
3.4059-3.52760.2991350.20782671X-RAY DIFFRACTION100
3.5276-3.66890.25151500.20252648X-RAY DIFFRACTION100
3.6689-3.83580.24821520.1882661X-RAY DIFFRACTION100
3.8358-4.0380.22821280.17812729X-RAY DIFFRACTION100
4.038-4.29090.18731390.17082665X-RAY DIFFRACTION100
4.2909-4.6220.21461380.15932691X-RAY DIFFRACTION99
4.622-5.08680.20551420.15392699X-RAY DIFFRACTION99
5.0868-5.82220.22841400.17342707X-RAY DIFFRACTION99
5.8222-7.33250.24631340.18862752X-RAY DIFFRACTION99
7.3325-54.63530.20661600.1942783X-RAY DIFFRACTION97
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)
10.1939-0.1204-0.10990.09160.0590.1016-0.03150.013-0.09780.0427-0.01810.0306-0.0291-0.0264-0.03910.0340.04280.0152-0.036-0.00060.0248-22.4269-14.256848.0535
20.1194-0.0068-0.00670.0864-0.04790.07670.0405-0.01380.0865-0.08020.02420.07030.05940.05460.01410.09150.0221-0.0250.06690.00060.0596-23.9407-26.849116.688
30.0775-0.09990.08790.1015-0.11590.12330.03070.21610.1151-0.0756-0.254-0.11820.0990.2158-0.2191-0.00940.1630.02550.24030.25960.0078-37.84664.3915-7.7085
40.1994-0.01630.01850.0496-0.0105-0.00290.02310.01880.0995-0.0618-0.03660.03510.0093-0.00850.0447-0.17110.0407-0.00130.0345-0.0040.0844-50.8694-0.05922.1295
50.0120.0619-0.06350.1499-0.12710.1432-0.0485-0.0187-0.0205-0.1023-0.0894-0.11170.05890.0252-0.1880.0234-0.02310.1364-0.03740.1109-0.04923.7906-4.21087.559
60.04560.0217-0.03740.06710.01250.1684-0.0098-0.02110.0445-0.0496-0.00780.028-0.00970.0877-0.02960.0122-0.0079-0.01740.05010.00780.00613.648410.02737.8405
70.05020.01340.02970.03780.07240.1133-0.1648-0.1307-0.04360.10680.03390.21740.0443-0.0113-0.0308-0.0040.17620.1494-0.0222-0.0070.1876-33.742528.091142.3305
80.0009-0.0211-0.00380.0723-0.0115-0.0118-0.0027-0.0283-0.0308-0.07280.00630.0501-0.01840.0067-0.01720.05040.0224-0.0598-0.06750.0459-0.0178-17.385431.371913.0497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:203)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 204:456)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 0:195)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 196:453)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 0:201)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 202:453)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 0:201)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 202:455)

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