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- PDB-3q10: Pantoate-beta-alanine ligase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3q10
TitlePantoate-beta-alanine ligase from Yersinia pestis
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
N-terminal domain of TfIIb - #60 / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / N-terminal domain of TfIIb / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Other non-globular / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...N-terminal domain of TfIIb - #60 / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / N-terminal domain of TfIIb / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Other non-globular / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Special / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / IMIDAZOLE / Pantothenate synthetase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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)130,27815
Polymers128,3244
Non-polymers1,95411
Water12,574698
1
A: Pantoate--beta-alanine ligase
C: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1458
Polymers64,1622
Non-polymers9836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-17 kcal/mol
Surface area25780 Å2
MethodPISA
2
B: Pantoate--beta-alanine ligase
D: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1337
Polymers64,1622
Non-polymers9715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-12 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.809, 77.241, 98.462
Angle α, β, γ (deg.)101.330, 94.910, 94.370
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#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)

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Non-polymers , 5 types, 709 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


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


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 698 / 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: 52.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 25% PEG-3350, 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 10, 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: 1.83→33.1 Å / Num. all: 109573 / Num. obs: 109573 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.044 / Χ2: 1.072 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.83-1.862.40.4582.0853871.00194.4
1.86-1.92.40.41553210.99795.1
1.9-1.932.50.3453991.00494.8
1.93-1.972.50.28453261.02794.9
1.97-2.012.60.25454111.01595.5
2.01-2.062.60.20953691.08695.2
2.06-2.112.60.15754331.02896.1
2.11-2.172.60.13954171.05696.1
2.17-2.232.60.11755241.06596.1
2.23-2.312.60.09754301.03297.1
2.31-2.392.60.08555081.12697.1
2.39-2.482.60.07555531.11297.4
2.48-2.62.60.06655091.09198.2
2.6-2.732.60.05955471.14398.2
2.73-2.92.60.05255701.17298.3
2.9-3.132.60.04555751.22498.4
3.13-3.442.60.0455811.15898.4
3.44-3.942.60.03255721.12899
3.94-4.972.50.02456311.05399
4.97-502.60.0255100.88597.6

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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: 1IHO

1iho


Resolution: 1.83→33.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.871 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 5527 5 %RANDOM
Rwork0.1736 ---
all0.1755 109539 --
obs0.1755 109539 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.56 Å2 / Biso mean: 36.882 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0.11 Å20.02 Å2
2---1.23 Å20.95 Å2
3---3.16 Å2
Refinement stepCycle: LAST / Resolution: 1.83→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8261 0 128 698 9087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228949
X-RAY DIFFRACTIONr_bond_other_d0.0010.026128
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.99412238
X-RAY DIFFRACTIONr_angle_other_deg0.96315011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82451158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70424.009429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.083151598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4611584
X-RAY DIFFRACTIONr_chiral_restr0.0980.21417
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021766
X-RAY DIFFRACTIONr_mcbond_it0.9021.55427
X-RAY DIFFRACTIONr_mcbond_other0.2871.52164
X-RAY DIFFRACTIONr_mcangle_it1.53628838
X-RAY DIFFRACTIONr_scbond_it2.3633522
X-RAY DIFFRACTIONr_scangle_it3.7584.53341
LS refinement shellResolution: 1.828→1.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 364 -
Rwork0.267 7204 -
all-7568 -
obs-7568 89.31 %
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)
10.68070.2659-0.04460.6183-0.05080.1745-0.0416-0.00830.13810.00170.00010.04360.0129-0.02690.04150.0406-0.0006-0.00330.0106-0.01990.093429.139259.637298.5246
21.4828-0.27560.06910.64790.07490.472-0.01930.35090.3751-0.0178-0.0607-0.0423-0.00770.06650.080.04570.004-0.00660.20670.10790.104828.286254.810865.4609
30.7321-0.40110.02421.62250.05690.5174-0.0323-0.164-0.07020.32090.0871-0.09380.1078-0.0271-0.05480.1365-0.0102-0.02550.05490.0150.024741.724728.0136116.1869
43.75090.8538-0.04312.189-0.68221.75340.07030.4037-0.632-0.130.13130.14970.4283-0.0964-0.20160.18290.0278-0.06730.224-0.08920.163615.537723.654362.4049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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