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- PDB-3mxt: Crystal Structure of Pantoate-Beta-alanine Ligase from Campylobac... -

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Basic information

Entry
Database: PDB / ID: 3mxt
TitleCrystal Structure of Pantoate-Beta-alanine Ligase from Campylobacter jejuni
ComponentsPantothenate synthetase
KeywordsLIGASE / alpha-beta-alpha / 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 / cytoplasm
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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Pantothenate synthetase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKim, Y. / Zhou, M. / Papazisi, L. / 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 Campylobacter jejuni
Authors: Kim, Y. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3959
Polymers32,9171
Non-polymers4788
Water6,575365
1
A: Pantothenate synthetase
hetero molecules

A: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,79118
Polymers65,8352
Non-polymers95616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area5690 Å2
ΔGint-82 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.314, 83.314, 148.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

21A-502-

HOH

31A-648-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 32917.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj0297c, panC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q9PIK2, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 6 types, 373 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 289 K / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 Tris pH 8.5, 20 % w/v PEG 8000, 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: 0.97926
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 26799 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 28.37 Å2 / Rsym value: 0.072 / Net I/σ(I): 21.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.91 / Rsym value: 0.621 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→27.49 Å / SU ML: 0.21 / Isotropic thermal model: mixed / σ(F): 0 / Phase error: 19.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.198 1328 5.02 %
Rwork0.159 --
obs0.161 26450 98.8 %
all-26450 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.816 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.1241 Å2-0 Å2-0 Å2
2--0.1241 Å20 Å2
3----0.2482 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 28 365 2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112422
X-RAY DIFFRACTIONf_angle_d1.2643269
X-RAY DIFFRACTIONf_dihedral_angle_d18.341923
X-RAY DIFFRACTIONf_chiral_restr0.088369
X-RAY DIFFRACTIONf_plane_restr0.005423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.92360.30871170.21062744X-RAY DIFFRACTION99
1.9236-2.01110.21931360.18342755X-RAY DIFFRACTION100
2.0111-2.11710.20411470.17272755X-RAY DIFFRACTION100
2.1171-2.24970.19981640.16462766X-RAY DIFFRACTION99
2.2497-2.42330.24571510.16312757X-RAY DIFFRACTION99
2.4233-2.6670.22591550.17062796X-RAY DIFFRACTION100
2.667-3.05240.2221600.16362809X-RAY DIFFRACTION99
3.0524-3.84410.17351620.14472830X-RAY DIFFRACTION99
3.8441-27.49570.16031360.14662910X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 4.7389 Å / Origin y: 29.9208 Å / Origin z: 80.3709 Å
111213212223313233
T0.1114 Å20.0174 Å20.0005 Å2-0.15 Å20.0012 Å2--0.1346 Å2
L0.3792 °2-0.6193 °20.0203 °2-1.3478 °20.3145 °2--0.3163 °2
S0.0129 Å °0.1116 Å °0.0203 Å °0.0712 Å °-0.0454 Å °-0.0741 Å °0.0151 Å °0.0786 Å °0.017 Å °
Refinement TLS groupSelection details: chain A

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