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- PDB-5hg0: Crystal Structure of Pantoate-beta-alanine Ligase from Francisell... -

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Basic information

Entry
Database: PDB / ID: 5hg0
TitleCrystal Structure of Pantoate-beta-alanine Ligase from Francisella tularensis complex with SAM
ComponentsPantothenate synthetase
KeywordsLIGASE / Pantoate-beta-alanine Ligase / Sructural 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 / 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
S-ADENOSYLMETHIONINE / Pantothenate synthetase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChang, C. / Maltseva, N. / Kim, Y. / 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 Francisella tularensis complex with SAM
Authors: Chang, C. / Maltseva, N. / Kim, Y. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Structure summary
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)61,2154
Polymers60,4182
Non-polymers7972
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-15 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.366, 47.366, 257.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#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
Details: N-terminal cloning artifact SNA
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: panC, FTT_1390 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5NF57, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M Sodium Tartrate, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 22727 / Num. obs: 22563 / % possible obs: 99.3 % / Redundancy: 5 % / Biso Wilson estimate: 31.02 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.04 / Rrim(I) all: 0.095 / Χ2: 0.799 / Net I/av σ(I): 14.884 / Net I/σ(I): 8.9 / Num. measured all: 113566
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.90.86210810.5810.4650.9830.74298.3
2.44-2.494.30.79811460.6470.4050.8980.80397.6
2.49-2.534.80.86711100.630.4240.9690.78299.4
2.53-2.5950.68811330.7470.3250.7640.77699.1
2.59-2.645.20.63811170.7010.2990.7070.7999
2.64-2.75.30.62711110.7930.2840.690.79899.4
2.7-2.775.40.48811360.8630.2210.5370.82199.5
2.77-2.855.40.38911270.870.1770.4290.80999.6
2.85-2.935.30.28311310.9190.1290.3130.77799.7
2.93-3.025.30.22811330.9350.1030.2520.82499.6
3.02-3.135.30.18111310.9410.0830.20.84399.8
3.13-3.265.20.14411070.9580.0660.1590.8799.7
3.26-3.4150.10711710.9410.050.1190.8699.9
3.41-3.585.10.09211160.9660.0430.1020.94199.7
3.58-3.8150.07511310.9710.0340.0830.86399.6
3.81-4.14.90.06711290.9710.0310.0740.87199.6
4.1-4.524.80.06211350.9790.0290.0690.82199.6
4.52-5.174.80.0611320.9770.0280.0670.78599.1
5.17-6.514.90.05211120.9780.0240.0580.6198.1
6.51-505.90.0511740.9910.0220.0550.60599.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
SBC-Collectdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N8H

3n8h


Resolution: 2.4→47.366 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 25.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2348 1100 5.28 %
Rwork0.1839 34584 -
obs0.1865 20806 81.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.67 Å2 / Biso mean: 41.9208 Å2 / Biso min: 2.85 Å2
Refinement stepCycle: final / Resolution: 2.4→47.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 0 54 110 4313
Biso mean--44.17 35.56 -
Num. residues----523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034289
X-RAY DIFFRACTIONf_angle_d0.5535815
X-RAY DIFFRACTIONf_chiral_restr0.044680
X-RAY DIFFRACTIONf_plane_restr0.003745
X-RAY DIFFRACTIONf_dihedral_angle_d16.0522641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.43770.3137320.259853156318
2.4377-2.50360.3127760.26281399147545
2.5036-2.57720.36191150.25322000211565
2.5772-2.66040.33321390.25722317245677
2.6604-2.75550.33211380.25182706284488
2.7555-2.86580.30251660.23852750291692
2.8658-2.99620.2551990.2232824302393
2.9962-3.15420.27241560.21322852300893
3.1542-3.35170.23851940.19252802299694
3.3517-3.61040.2631370.17372844298193
3.6104-3.97360.22491650.15892880304594
3.9736-4.54820.16441620.14032830299294
4.5482-5.72870.19451350.1482876301194
5.7287-47.37540.16611150.16342973308896
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)
11.31560.09590.22381.9382-0.13251.73430.164-0.2698-0.2579-0.0909-0.1797-0.38170.5298-0.3644-0.02880.2721-0.1777-0.11820.27310.06860.238312.5552-16.606394.1292
21.73180.52590.43321.82160.14411.5555-0.1608-0.07010.1095-0.08630.18470.44660.1725-0.57860.03620.2502-0.1242-0.04930.46450.07890.30943.905-8.322292.3537
31.0515-0.8049-0.28450.8570.36662.8904-0.26560.15360.38610.12460.04290.0827-0.3101-0.4725-0.07870.26570.009-0.12450.35190.05810.202616.42050.3354105.3432
40.67820.2198-0.20770.2994-0.04171.0211-0.23120.09910.13990.0139-0.10710.0192-0.1195-0.3276-0.15580.176-0.0644-0.19670.30160.10430.262818.5150.713397.3435
51.4881-0.26070.53342.9437-0.03191.1587-0.01520.2684-0.1275-0.1708-0.4096-0.21660.08630.28580.07160.2535-0.0569-0.02390.19390.02730.24321.1486-8.441589.5876
60.2955-0.28320.1420.96050.06451.8536-0.09310.0795-0.05350.03330.03170.0328-0.05770.12280.01890.1827-0.0462-0.05370.19130.09580.221818.5572-4.393687.4924
76.54260.25940.492.6392-0.09340.4030.07250.40370.1546-0.5985-0.06020.4489-0.4328-0.2524-0.02230.4619-0.038-0.13950.31010.01990.29278.53297.391871.1314
81.8256-0.5437-0.22521.25260.45971.50810.16010.18150.3761-0.3827-0.1916-0.2386-0.4737-0.1613-0.12520.4918-0.145-0.02670.40590.21090.420417.697516.13972.3071
93.83620.00960.19532.8032-0.41122.0175-0.31950.13140.34440.1594-0.1359-0.3362-0.42120.2690.14230.2701-0.0665-0.08560.28680.10170.357517.55558.060679.7292
102.4015-0.4514-0.07411.8157-0.17973.76080.30840.599-0.3359-0.4246-0.1120.20430.46010.1-0.02980.40560.1608-0.02420.35410.03590.330338.5298-20.138110.8771
111.5109-0.31850.96061.01640.1072.8858-0.16330.02690.27350.1404-0.0674-0.1293-0.05970.24710.0970.1233-0.0181-0.0410.1530.09520.206133.9825-5.0717118.6297
121.96590.56282.03651.0083-0.35113.6321-0.0681-0.26120.124-0.01370.04050.19520.2006-0.53350.00220.1765-0.0724-0.00670.28060.03850.197320.7808-8.4927117.9496
131.5017-0.362-1.31691.6253-1.32382.8966-0.2412-0.02620.09710.0697-0.2717-0.724-0.1330.23850.07540.24130.0369-0.03330.26050.03890.28737.09170.3784134.757
141.8486-1.86270.03832.8127-0.04920.7611-0.6767-0.68660.54381.08190.3879-0.2418-0.324-0.0182-0.21530.69680.2853-0.14230.3454-0.15470.406929.55511.344142.6605
153.43790.4772-0.38783.0696-0.00782.6477-0.20930.06960.27210.0702-0.17050.0412-0.4614-0.49830.11230.29230.0589-0.11280.2979-0.04370.404826.49036.9965134.2845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 60 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 93 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 112 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 139 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 152 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 192 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 193 through 208 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 209 through 224 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 225 through 260 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 22 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 23 through 152 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 153 through 173 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 174 through 192 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 193 through 224 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 225 through 261 )B0

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