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

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Basic information

Entry
Database: PDB / ID: 3qtt
TitleCrystal Structure of Pantoate-beta-alanine Ligase from Francisella tularensis Complexed with Beta-gamma ATP and Beta-alanine
ComponentsPantothenate synthetase
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta sandwich / cytosol
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / BETA-ALANINE / PROLINE / Pantothenate synthetase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.599 Å
AuthorsMaltseva, N. / Kim, Y. / 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 Francisella tularensis Complexed with Beta-gamma ATP and Beta-alanine.
Authors: Maltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionFeb 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: 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)61,8639
Polymers60,4182
Non-polymers1,4457
Water1,910106
1
A: Pantothenate synthetase
hetero molecules

B: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8639
Polymers60,4182
Non-polymers1,4457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-y+1,x,z-1/41
Buried area4340 Å2
ΔGint-32 kcal/mol
Surface area22580 Å2
MethodPISA
2
A: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9445
Polymers30,2091
Non-polymers7354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9204
Polymers30,2091
Non-polymers7103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.147, 47.147, 257.661
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: SCHU S4 / Gene: FTT_1390, panC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q5NF57, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 5 types, 113 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BAL / BETA-ALANINE / Β-Alanine


Type: peptide-like / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
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: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 17255 / Num. obs: 17255 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.091 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.759 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
RESOLVEmodel building
BUCCANEERmodel building
PHENIX(phenix.refine: dev_601)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RESOLVEphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.599→33.338 Å / SU ML: 0.43 / Isotropic thermal model: mixed / σ(F): 0.4 / Phase error: 28.37 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2513 1668 9.9 %
Rwork0.168 --
obs0.1764 16845 97.84 %
all-16845 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.732 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0132 Å20 Å2-0 Å2
2--4.0132 Å2-0 Å2
3----8.0263 Å2
Refinement stepCycle: LAST / Resolution: 2.599→33.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4173 0 91 106 4370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124428
X-RAY DIFFRACTIONf_angle_d1.6346012
X-RAY DIFFRACTIONf_dihedral_angle_d19.1791714
X-RAY DIFFRACTIONf_chiral_restr0.109689
X-RAY DIFFRACTIONf_plane_restr0.008774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5987-2.67510.41241310.25051200X-RAY DIFFRACTION93
2.6751-2.76140.3751330.2351253X-RAY DIFFRACTION95
2.7614-2.86010.35431350.22481202X-RAY DIFFRACTION95
2.8601-2.97450.32751370.2111240X-RAY DIFFRACTION97
2.9745-3.10980.3291440.21671269X-RAY DIFFRACTION98
3.1098-3.27360.30251450.21371254X-RAY DIFFRACTION98
3.2736-3.47850.30341410.18671288X-RAY DIFFRACTION99
3.4785-3.74680.27611440.16751286X-RAY DIFFRACTION100
3.7468-4.12320.23531360.15251280X-RAY DIFFRACTION100
4.1232-4.71840.20191400.12581330X-RAY DIFFRACTION100
4.7184-5.93920.23931400.15721289X-RAY DIFFRACTION100
5.9392-33.34070.18961420.15271286X-RAY DIFFRACTION99
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)
10.58480.59410.06581.80840.87331.91470.0748-0.1960.0784-0.1627-0.2990.2343-0.0482-0.13170.15650.2939-0.0195-0.07930.3672-0.0580.35561.937631.5527134.087
20.3520.13721.34021.0176-0.2042.4443-0.2621-0.2016-0.0106-0.1843-0.013-0.04340.024-0.16590.04560.1768-0.0067-0.04910.2664-0.00740.148513.77343.8134163.5845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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