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- PDB-3q12: Pantoate-beta-alanine ligase from Yersinia pestis in complex with... -

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Basic information

Entry
Database: PDB / ID: 3q12
TitlePantoate-beta-alanine ligase from Yersinia pestis in complex with pantoate.
ComponentsPantoate--beta-alanine ligase
KeywordsLIGASE / 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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PANTOATE / Pantothenate synthetase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsOsipiuk, J. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Pantoate-beta-alanine ligase from Yersinia pestis.
Authors: Osipiuk, J. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionDec 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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: Pantoate--beta-alanine ligase
B: Pantoate--beta-alanine ligase
C: Pantoate--beta-alanine ligase
D: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,98310
Polymers128,3244
Non-polymers6606
Water20,7891154
1
A: Pantoate--beta-alanine ligase
B: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4925
Polymers64,1622
Non-polymers3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-8 kcal/mol
Surface area26000 Å2
MethodPISA
2
C: Pantoate--beta-alanine ligase
D: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4925
Polymers64,1622
Non-polymers3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-10 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.730, 77.054, 98.757
Angle α, β, γ (deg.)100.670, 95.330, 94.430
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 32080.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: panC, y0785, YPO3402, YP_0283 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZBK7, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical
ChemComp-PAF / PANTOATE / 2,4-DIHYDROXY-3,3-DIMETHYL-BUTYRATE


Mass: 147.149 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1154 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 20% PEG-5000 MME, pH 6.5, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.58→36.7 Å / Num. all: 153768 / Num. obs: 153768 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.042 / Χ2: 1.217 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.58-1.611.90.2672.9436910.95141.7
1.61-1.641.90.24641340.92847.2
1.64-1.671.90.21248770.99855.4
1.67-1.71.90.18656730.97164.6
1.7-1.741.90.16470731.03780.1
1.74-1.781.90.14383421.06294.9
1.78-1.822.10.12583891.1195.7
1.82-1.872.20.10585591.13896.3
1.87-1.932.20.08884461.23296.3
1.93-1.992.20.07484671.24496.7
1.99-2.062.20.06485161.25696.8
2.06-2.142.20.05685941.30896.9
2.14-2.242.20.04985181.25997.3
2.24-2.362.20.04386041.29697.4
2.36-2.512.20.04185301.31797.7
2.51-2.72.20.03986431.28198
2.7-2.972.20.03786981.22798.3
2.97-3.42.20.03786461.27898.5
3.4-4.292.20.03586651.31298.7
4.29-502.20.03887031.39198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q10

3q10


Resolution: 1.58→36.69 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.052 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 7730 5 %RANDOM
Rwork0.1496 ---
all0.1519 153765 --
obs0.1519 153765 87.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 129.03 Å2 / Biso mean: 28.2763 Å2 / Biso min: 8.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.04 Å20.26 Å2
2---0.93 Å20.92 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 1.58→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8920 0 42 1154 10116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0229678
X-RAY DIFFRACTIONr_bond_other_d0.0010.026643
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.98313261
X-RAY DIFFRACTIONr_angle_other_deg0.984316324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7451288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28224.222469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.543151771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.071588
X-RAY DIFFRACTIONr_chiral_restr0.2250.21538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021890
X-RAY DIFFRACTIONr_mcbond_it1.7661.55918
X-RAY DIFFRACTIONr_mcbond_other0.5621.52359
X-RAY DIFFRACTIONr_mcangle_it2.75829652
X-RAY DIFFRACTIONr_scbond_it4.11833760
X-RAY DIFFRACTIONr_scangle_it6.1894.53528
X-RAY DIFFRACTIONr_rigid_bond_restr1.676316321
LS refinement shellResolution: 1.579→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 271 -
Rwork0.272 5146 -
all-5417 -
obs-5417 41.52 %

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