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- PDB-3uk2: The structure of Pantothenate synthetase from Burkholderia thaila... -

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Basic information

Entry
Database: PDB / ID: 3uk2
TitleThe structure of Pantothenate synthetase from Burkholderia thailandensis
ComponentsPantothenate synthetase
KeywordsLIGASE / AMP / Pantothenate synthetase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / cytosol
Similarity search - Function
Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich ...Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / D-MALATE / Pantothenate synthetase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionNov 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Pantothenate synthetase
B: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,70712
Polymers63,4792
Non-polymers1,22910
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-28 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.910, 166.910, 166.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pantothenate synthetase / PS / Pantoate--beta-alanine ligase / Pantoate-activating enzyme


Mass: 31739.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: panC, BTH_I0848 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2T095, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 5 types, 368 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: ButhA.00097.a 51.6 mg/ml, 0.1M MMT buffer, 25% PEG1500. Cryoprotection 25% ethylene glycol, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.25→118.02 Å / Num. obs: 36697 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.581 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.25-2.310.4714.45202462690100
2.31-2.370.3975.31197792630100
2.37-2.440.3565.93190482536100
2.44-2.520.2947.12189312514100
2.52-2.60.2528.34179172380100
2.6-2.690.2249.3176482343100
2.69-2.790.19910.43168332235100
2.79-2.90.15113.59164632184100
2.9-3.030.12716.32155362070100
3.03-3.180.09520.314968198699.9
3.18-3.350.07126.48143031894100
3.35-3.560.05432.92135201800100
3.56-3.80.04439.55128501710100
3.8-4.110.03945.1911633155499.9
4.11-4.50.03250.54109091463100
4.5-5.030.02954.499842132099.9
5.03-5.810.03447.098667116699.9
5.81-7.120.03448.23734099999.9
7.12-10.060.02362.5559378499.7
10.060.02268.31256843995.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.61 Å
Translation2.5 Å44.61 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→41.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.1997 / WRfactor Rwork: 0.1614 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8708 / SU B: 8.521 / SU ML: 0.12 / SU R Cruickshank DPI: 0.2275 / SU Rfree: 0.1919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 1833 5 %RANDOM
Rwork0.1785 ---
obs0.1808 36673 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.91 Å2 / Biso mean: 27.2526 Å2 / Biso min: 10.56 Å2
Refinement stepCycle: LAST / Resolution: 2.25→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 76 358 4792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194541
X-RAY DIFFRACTIONr_bond_other_d0.0010.023120
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9936172
X-RAY DIFFRACTIONr_angle_other_deg0.94337564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0325568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46623.163215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43415760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3391551
X-RAY DIFFRACTIONr_chiral_restr0.0830.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02927
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 151 -
Rwork0.203 2433 -
all-2584 -
obs--100 %
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)
11.06730.25680.05990.68640.11041.48210.0748-0.00620.0266-0.0014-0.05120.0672-0.0725-0.1003-0.02350.0907-0.0146-0.01470.0520.00110.082937.3088-11.9895-45.6484
23.7942-4.4519-1.19559.87032.92943.0363-0.04440.09070.0477-0.0904-0.0934-0.0838-0.0342-0.06210.13770.0715-0.0021-0.02970.06440.01810.089335.9712-16.2323-51.5817
30.3227-0.1093-0.07280.30810.23411.7870.01270.0295-0.0370.02140.03210.0111-0.01520.0612-0.04490.0924-0.0229-0.0110.0652-0.00650.081249.0536-16.2383-39.3604
41.71750.5913-0.01621.3208-0.43691.0601-0.0121-0.0140.01350.10970.0231-0.122-0.04660.0704-0.0110.1148-0.0108-0.0280.0613-0.01530.071558.0705-14.961-23.4589
51.38311.3833-0.28611.8999-0.17071.5165-0.0294-0.0289-0.18850.17-0.0418-0.32730.08990.06210.07120.1151-0.008-0.05880.02590.02690.14270.601610.1757-23.8171
61.72210.2178-0.21612.45610.14041.32590.0458-0.0831-0.0460.525-0.1417-0.22210.03280.03590.09590.2156-0.062-0.08050.06530.01080.045764.894915.3893-13.4218
70.83030.4018-0.05061.3283-0.23830.14330.03110.07680.05160.1288-0.03630.01560.0326-0.02130.00520.1406-0.0394-0.00320.0562-0.01760.07155.761217.2458-26.121
81.09090.27490.89261.23030.21162.45480.0727-0.05070.02110.1626-0.10910.22570.0133-0.10410.03640.1277-0.02350.06540.0237-0.03020.099138.59127.872-23.521
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 80
2X-RAY DIFFRACTION2A81 - 97
3X-RAY DIFFRACTION3A98 - 198
4X-RAY DIFFRACTION4A199 - 279
5X-RAY DIFFRACTION5B0 - 51
6X-RAY DIFFRACTION6B52 - 97
7X-RAY DIFFRACTION7B98 - 185
8X-RAY DIFFRACTION8B186 - 279

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