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- PDB-7tot: Crystal Structure of pantothenate synthetase from Bartonella henselae -

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Basic information

Entry
Database: PDB / ID: 7tot
TitleCrystal Structure of pantothenate synthetase from Bartonella henselae
ComponentsPantothenate synthetase
KeywordsLIGASE / SSGCID / pantothenate synthetase / pantoate--beta-alanine ligase / ATP binding / nucleotide binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
NITRATE ION / Pantothenate synthetase
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal Structure of pantothenate synthetase from Bartonella henselae
Authors: Bolejack, M.J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)67,81215
Polymers66,7142
Non-polymers1,09913
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-78 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.820, 51.260, 78.650
Angle α, β, γ (deg.)108.900, 99.370, 90.600
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 33356.801 Da / Num. of mol.: 2 / Fragment: BaheA.00498.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1) (bacteria)
Strain: ATCC 49882 / DSM 28221 / Houston 1 / Gene: panC, BH05120 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6G456, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 52.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein at 21 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 12.5% w/v PEG 1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0.03 M each sodium nitrate, disodium hydrogen phosphate, ...Details: Protein at 21 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 12.5% w/v PEG 1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0.03 M each sodium nitrate, disodium hydrogen phosphate, and ammonium sulfate, and 0.1 M MES/imidazole pH 7.5 (Morpheus C8). Cryo: Direct. Tray: 320104c8: pin: ifl7-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 1, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→35.35 Å / Num. obs: 58720 / % possible obs: 94.9 % / Redundancy: 2.193 % / Biso Wilson estimate: 29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.023 / Rrim(I) all: 0.031 / Χ2: 0.945 / Net I/σ(I): 19.95 / Num. measured all: 128748 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.852.2140.3492.79648460243570.8950.4794.7
1.85-1.92.2050.2743.479331446942320.9320.37194.7
1.9-1.952.2130.1974.718974431940550.960.26693.9
1.95-2.012.210.1495.968823421439920.9740.20194.7
2.01-2.082.2140.1038.158514408738460.9880.13994.1
2.08-2.152.2090.0829.948238393637300.9930.11194.8
2.15-2.232.2010.06212.537999383036340.9950.08494.9
2.23-2.322.2010.05315.057661367834800.9960.07294.6
2.32-2.432.2050.04517.287363350433390.9970.0695.3
2.43-2.552.1980.03520.717072339632180.9980.04794.8
2.55-2.682.1940.0323.796616316430150.9980.04195.3
2.68-2.852.1840.02527.936262303228670.9990.03494.6
2.85-3.042.1870.02134.135897282526960.9990.02995.4
3.04-3.292.1730.01838.825540266625500.9990.02495.6
3.29-3.62.1670.01543.435040242523260.9990.02195.9
3.6-4.022.1520.01547.514520218521000.9990.0296.1
4.02-4.652.1540.01450.394067197018880.9990.01995.8
4.65-5.692.150.01250.513380163115720.9990.01696.4
5.69-8.052.1290.01250.582566124412050.9990.01796.9
8.05-35.352.0020.0135212377016180.9990.01788.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX4438refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ejc

2ejc


Resolution: 1.8→35.35 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 2089 3.56 %
Rwork0.1786 56580 -
obs0.1798 58669 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.73 Å2 / Biso mean: 45.4034 Å2 / Biso min: 17.09 Å2
Refinement stepCycle: final / Resolution: 1.8→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 70 373 4759
Biso mean--48.55 44.8 -
Num. residues----566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.3221610.27693757391894
1.84-1.890.33081550.26143696385194
1.89-1.940.24861230.23723750387394
1.94-20.25641450.23253776392195
2-2.060.2251410.21013750389194
2.06-2.130.23991620.20063726388894
2.13-2.220.21511170.19663817393495
2.22-2.320.24421280.2013771389995
2.32-2.440.26331320.19553770390295
2.44-2.60.23781450.19613730387595
2.6-2.80.21781470.1983781392895
2.8-3.080.18571840.19043761394595
3.08-3.520.27171300.1723819394996
3.52-4.440.19781190.1473842396196
4.44-35.350.14451000.14813834393495
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)
12.59960.2813-0.17522.418-0.16853.8596-0.07780.1770.0161-0.2616-0.0285-0.23-0.06710.44960.08180.1613-0.00920.01620.24040.01080.1764-0.3539-1.42120.4709
23.28420.108-0.23375.04573.16986.8370.09130.3897-0.2623-0.4586-0.33690.16520.0236-0.78430.21080.5795-0.040.02660.5615-0.11110.2677-7.4507-13.2372-26.2224
31.66311.704-0.11621.6379-0.25034.2075-0.0941-0.35420.09180.0592-0.48160.51730.8616-1.23340.5120.5757-0.1160.04240.782-0.22670.3883-11.4989-16.5858-18.9746
42.833-0.1334-0.04692.850.09733.9943-0.0491-0.18430.33420.3216-0.12090.2239-0.5798-0.63250.13550.2680.084-0.00530.31-0.07120.2648-20.99766.630620.8306
53.5246-0.3788-0.40382.83780.26484.2017-0.1432-0.3509-0.41880.5053-0.05270.82670.4591-1.1850.21240.3496-0.05620.16150.7996-0.03030.4578-30.5124-5.255923.9722
62.7599-0.48430.05393.30390.36924.2999-0.0914-0.1857-0.15910.3299-0.05950.1120.3101-0.19480.10720.1721-0.02860.03090.2073-0.01080.1714-14.1212-5.853118.8999
73.3764-0.116-0.9964.3136-2.83098.42420.1136-0.4262-0.290.2334-0.4253-0.24660.33850.9590.18890.5520.04610.03510.52390.11660.2719-11.1313-13.177146.9519
81.5036-0.56851.19630.69320.05141.4412-0.18590.3617-0.0199-0.0599-0.6498-0.52251.01381.62860.48160.73390.25770.15430.99420.32410.5015-3.861-17.831838.6578
93.1729-0.9188-0.94513.4492-1.49417.07340.03210.1324-0.2542-0.2399-0.4357-0.4081.07561.01190.64090.65950.04420.03810.53840.10620.3087-11.427-15.306540.6744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 173 )A0 - 173
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 233 )A174 - 233
3X-RAY DIFFRACTION3chain 'A' and (resid 234 through 282 )A234 - 282
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 61 )B0 - 61
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 84 )B62 - 84
6X-RAY DIFFRACTION6chain 'B' and (resid 85 through 173 )B85 - 173
7X-RAY DIFFRACTION7chain 'B' and (resid 174 through 233 )B174 - 233
8X-RAY DIFFRACTION8chain 'B' and (resid 234 through 260 )B234 - 260
9X-RAY DIFFRACTION9chain 'B' and (resid 261 through 282 )B261 - 282

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