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- PDB-7t88: Crystal Structure of the C-terminal Domain of the Phosphate Acety... -

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Basic information

Entry
Database: PDB / ID: 7t88
TitleCrystal Structure of the C-terminal Domain of the Phosphate Acetyltransferase from Escherichia coli
ComponentsPhosphate acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phosphate acetyltransferase activity / phosphate acetyltransferase / acetyl-CoA biosynthetic process / cytoplasm
Similarity search - Function
Phosphate acetyltransferase, bacteria / DRTGG / DRTGG domain / Phosphate acetyltransferase / HPr(Ser) kinase/phosphorylase-like, N-terminal domain superfamily / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IODIDE ION / : / PHOSPHATE ION / Phosphate acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKim, Y. / Dementiev, A. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
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 c from Escherichia coli
Authors: Kim, Y. / Dementiev, A. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,01312
Polymers35,2231
Non-polymers79011
Water81145
1
A: Phosphate acetyltransferase
hetero molecules

A: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,02524
Polymers70,4462
Non-polymers1,57922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6630 Å2
ΔGint-65 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.875, 72.875, 193.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphate acetyltransferase / Phosphotransacetylase


Mass: 35223.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: WR15_08840 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: A0A0H0GLE6, phosphate acetyltransferase

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Non-polymers , 7 types, 56 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.67 Å3/Da / Density % sol: 66.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Bis-Tris:HCl pH 6.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 31287 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 54.54 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.159 / Net I/σ(I): 24.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.642 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 1515 / CC1/2: 0.535 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpha Fold2

Resolution: 2.1→48.26 Å / SU ML: 0.2286 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 1473 4.72 %
Rwork0.1999 29702 -
obs0.2013 31175 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 31 45 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232501
X-RAY DIFFRACTIONf_angle_d0.5343396
X-RAY DIFFRACTIONf_chiral_restr0.0416405
X-RAY DIFFRACTIONf_plane_restr0.0051447
X-RAY DIFFRACTIONf_dihedral_angle_d12.2096938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.26321110.2792597X-RAY DIFFRACTION97.73
2.17-2.250.26821390.23662636X-RAY DIFFRACTION99.96
2.25-2.340.24781310.23442653X-RAY DIFFRACTION100
2.34-2.440.26441220.23042683X-RAY DIFFRACTION100
2.44-2.570.25881290.22322654X-RAY DIFFRACTION100
2.57-2.730.30011490.25122659X-RAY DIFFRACTION100
2.73-2.950.26941550.23982670X-RAY DIFFRACTION100
2.95-3.240.24261490.23352685X-RAY DIFFRACTION100
3.24-3.710.24761090.20322764X-RAY DIFFRACTION100
3.71-4.670.1881310.16662770X-RAY DIFFRACTION100
4.67-48.260.21951480.18322931X-RAY DIFFRACTION99.81
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)
13.391783965850.05963781703533.339796166791.8678569394-0.6676224381537.18857261670.3600481983030.257919837618-0.194138523771-0.1383326339150.0823783611243-0.1314783825520.9430395169440.538378483044-0.4356793941880.7168769830040.063085657869-0.08385103584980.462541205046-0.08172006721780.623522198151-12.8750339345-12.04336350325.7516131306
27.833225533460.34564956738-3.639242924136.46458999582-2.597302804159.84676558361-0.2034947305710.866127835935-0.043933428141-1.316986422420.012479595376-0.8020847642110.8204781846360.6301250468940.04638040085280.927256637038-0.010794343044-0.1127096142470.664185442798-0.07448413140030.62781360959-11.8538700885-8.5011526758112.3985036075
34.71890705078-2.876689725040.4914553340756.780684600030.4628097650725.09821889802-0.3679919692670.157498383180.283492136777-0.9944422264530.3713294119070.1721824880190.01632823836790.6245403113440.01016821104440.834034238257-0.188083695593-0.1795785840550.6321483962810.03419655754680.537320164496-24.489121355-3.3459327630910.9322635711
42.01625507425-0.143059969798-2.507780940546.43704792584-1.392004376826.30285925899-0.04147629995570.9633205118410.634654616421-0.6168684365440.1457932712210.915119467338-0.359892224966-0.47172029886-0.1964548972171.2199356584-0.0657126951952-0.399848861150.624827366350.01058915810961.02383898454-31.559686777211.006587208313.670998168
51.872328202510.5246114553921.78598099742.069165206930.3667864383944.922383400070.0406484763142-0.192371701201-0.0399475197242-0.2676144827180.1140324125350.390939357040.0391569323391-0.428656714598-0.1382782575050.443433369242-0.0312571576229-0.0922691480490.4383086017470.0115611068330.533085094679-21.4016280010.56702575852833.3614465618
64.62835585867-0.136649739643-0.4768578822945.034465389051.429935549473.610616150910.174999138521-0.491752172624-0.1893851779360.34075346552-0.05238266615730.2218027793770.164565947146-0.440454654585-0.1364015459610.550867991789-0.02493757864390.02431527069190.6037763911280.07041822224020.398239042904-19.72606691511.0767298663956.0756808302
74.456979173041.070772661281.094155614498.18724277276-3.277643755316.098113037120.219273136844-0.233466417202-0.2835017761480.376994258739-0.0447070072116-0.1142124358650.0637294638638-0.240466051143-0.1905568343590.430329674180.0157981289633-0.04864346569150.455804292821-0.07092374651930.359852684741-11.63417584571.3809314199349.3297905197
86.692072857011.65454710351-3.426108639638.47821805191-0.630590207014.27149973884-0.4217827714470.2571431713950.869254001173-0.2196114598730.488887496069-0.4690829276410.170574867220.372320066135-0.01552217945240.485857156058-0.034764589612-0.06722270139270.450264091653-0.07259218746850.414522188164-14.3413108789-1.4270595191831.8945654634
96.847660289072.27488825263-4.853151721726.43125785889-1.937538584363.55258629585-0.117228730222-0.2523721120560.1408453501240.2151414753570.4023793633050.06077118547440.3861514350130.178064514684-0.3153603031570.579490596798-0.00793741787902-0.1622480377440.484158800657-0.05681166946910.511887002958-16.3685516822-8.979194382929.3064990071
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 387 through 426 )387 - 4261 - 40
22chain 'A' and (resid 427 through 448 )427 - 44841 - 62
33chain 'A' and (resid 449 through 475 )449 - 47563 - 89
44chain 'A' and (resid 476 through 492 )476 - 49290 - 106
55chain 'A' and (resid 493 through 580 )493 - 580107 - 194
66chain 'A' and (resid 581 through 639 )581 - 639195 - 253
77chain 'A' and (resid 640 through 670 )640 - 670254 - 284
88chain 'A' and (resid 671 through 695 )671 - 695285 - 309
99chain 'A' and (resid 696 through 713 )696 - 713310 - 327

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