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- PDB-3mue: Crystal Structure of Pantoate-beta-Alanine Ligase from Salmonella... -

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Basic information

Entry
Database: PDB / ID: 3mue
TitleCrystal Structure of Pantoate-beta-Alanine Ligase from Salmonella typhimurium
ComponentsPantothenate synthetase
KeywordsLIGASE / alpha-beta fold / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
ACETIC ACID / ETHANOL / Pantothenate synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Pantoate-beta-Alanine Ligase from Salmonella typhimurium
Authors: Kim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Pantothenate synthetase
B: Pantothenate synthetase
C: Pantothenate synthetase
D: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,63628
Polymers128,6804
Non-polymers1,95624
Water6,107339
1
A: Pantothenate synthetase
B: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,51317
Polymers64,3402
Non-polymers1,17315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-17 kcal/mol
Surface area27130 Å2
MethodPISA
2
C: Pantothenate synthetase
D: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,12311
Polymers64,3402
Non-polymers7839
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-3 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.226, 134.923, 93.923
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 32170.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: panC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: Q8ZRR1, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 5 types, 363 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS pH 8.5, 20 %v/v Ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 14, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 53465 / Num. obs: 53465 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 58.92 Å2 / Rsym value: 0.099 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2715 / Rsym value: 0.708 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1IHO

1iho


Resolution: 2.701→35.387 Å / SU ML: 0.41 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2713 5.08 %random
Rwork0.178 ---
all0.181 53367 --
obs0.181 53367 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.36 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 64.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.3434 Å20 Å20.2522 Å2
2--1.3483 Å2-0 Å2
3----0.0049 Å2
Refinement stepCycle: LAST / Resolution: 2.701→35.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8947 0 125 339 9411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019303
X-RAY DIFFRACTIONf_angle_d1.2812554
X-RAY DIFFRACTIONf_dihedral_angle_d19.1793560
X-RAY DIFFRACTIONf_chiral_restr0.0771438
X-RAY DIFFRACTIONf_plane_restr0.0071636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.701-2.79720.33242290.2514646487591
2.7972-2.90910.30782740.239550705344100
2.9091-3.04150.28672700.216551245394100
3.0415-3.20170.26882520.203250805332100
3.2017-3.40220.26452850.197351065391100
3.4022-3.66460.23062770.177150905367100
3.6646-4.03290.20862670.148751335400100
4.0329-4.61540.1772940.126950975391100
4.6154-5.81080.22900.149951245414100
5.8108-35.39050.21712750.1795184545999
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)
11.51180.6465-0.14371.94670.13350.72130.056-0.0204-0.00670.1226-0.07590.0442-0.20560.03850.01810.12930.0152-0.04340.01640.00680.067926.35050.463513.0325
20.9339-0.3703-0.53922.79030.52431.868-0.054-0.0076-0.1837-0.1209-0.06770.09470.2377-0.05250.1090.12920.0392-0.08790.0818-0.02860.198826.1652-38.07775.3913
31.9361.4648-1.5812.6289-1.69151.47830.03410.31470.00830.03690.16660.0491-0.117-0.2021-0.14260.2187-0.13720.02680.3904-0.02890.14619.96215.7902-26.9621
40.30420.5659-0.71611.565-0.99511.50390.0746-0.01640.10610.03780.12220.0759-0.2606-0.2019-0.15140.5431-0.14960.06410.5240.08750.335639.29428.5016-51.8758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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