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- PDB-3n8h: Crystal Structure of Pantoate-beta-alanine Ligase from Francisell... -

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Basic information

Entry
Database: PDB / ID: 3n8h
TitleCrystal Structure of Pantoate-beta-alanine Ligase from Francisella tularensis
ComponentsPantothenate synthetase
KeywordsLIGASE / alpha-beta sandwich / Structural Genomics / structural genomics of infectious diseases / 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 / ADENOSINE MONOPHOSPHATE / PROLINE / Pantothenate synthetase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsMaltseva, N. / Kim, Y. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2010
Title: Crystal Structure of Pantoate-beta-alanine Ligase from Francisella tularensis
Authors: Maltseva, N. / Kim, Y. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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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)61,77111
Polymers60,4182
Non-polymers1,3539
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-15 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 47.200, 259.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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: 30209.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: tularensis SCHU S4 / Gene: FTT_1390, panC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: Q5NF57, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 5 types, 340 molecules

#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Proline, 0.1 M HEPES pH 7.5, 10 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 37865 / Num. obs: 37865 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 35.63 Å2 / Rsym value: 0.106 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1913 / Rsym value: 0.718 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
RESOLVEmodel building
BUCCANEERmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RESOLVEphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.001→32.323 Å / SU ML: 0.23 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1888 5 %random
Rwork0.179 ---
all0.18 37792 --
obs0.18 37792 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.559 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.001→32.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 88 331 4615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014494
X-RAY DIFFRACTIONf_angle_d1.2036099
X-RAY DIFFRACTIONf_dihedral_angle_d22.1661755
X-RAY DIFFRACTIONf_chiral_restr0.078701
X-RAY DIFFRACTIONf_plane_restr0.006787
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.001-2.07230.26981850.22253615380099
2.0723-2.15530.26452060.196936233829100
2.1553-2.25340.25661760.186435673743100
2.2534-2.37210.2611850.188936293814100
2.3721-2.52070.25721880.1935583746100
2.5207-2.71520.23241900.186535923782100
2.7152-2.98830.25451980.179136173815100
2.9883-3.42030.21261920.192536093711100
3.4203-4.30760.20691840.16413579376399
4.3076-32.32740.19121840.15683515369997
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)
10.86960.10080.51960.8323-0.43141.8439-0.0324-0.03180.0403-0.01130.02020.03350.1108-0.10120.01270.253-0.0488-0.00810.24560.02470.234820.1446-9.330441.5686
20.7017-0.2942-0.44790.819-0.4172.16880.01640.05490.0523-0.0422-0.0791-0.09750.01210.01080.05840.25140.0202-0.04360.2540.02630.25820.83097.75546.0389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0 - 275
2X-RAY DIFFRACTION2chain BB0 - 275

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