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- PDB-2af3: Phosphotransacetylase from Methanosarcina thermophila soaked with... -

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Basic information

Entry
Database: PDB / ID: 2af3
TitlePhosphotransacetylase from Methanosarcina thermophila soaked with Coenzyme A
ComponentsPhosphate acetyltransferase
KeywordsTRANSFERASE / Pta dimer soaked with Coenzyme A / acyltransferase
Function / homology
Function and homology information


phosphate acetyltransferase activity / phosphate acetyltransferase / acetyl-CoA biosynthetic process / plasma membrane
Similarity search - Function
Isocitrate/Isopropylmalate dehydrogenase-like / Rossmann fold - #10950 / Phosphate acetyltransferase / Phosphate acetyl/butyryltransferase / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Rossmann fold ...Isocitrate/Isopropylmalate dehydrogenase-like / Rossmann fold - #10950 / Phosphate acetyltransferase / Phosphate acetyl/butyryltransferase / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Phosphate acetyltransferase
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLawrence, S.H. / Luther, K.B. / Ferry, J.G. / Schindelin, H.
Citation
Journal: J.Bacteriol. / Year: 2006
Title: Structural and functional studies suggest a catalytic mechanism for the phosphotransacetylase from Methanosarcina thermophila.
Authors: Lawrence, S.H. / Luther, K.B. / Schindelin, H. / Ferry, J.G.
#1: Journal: Structure / Year: 2004
Title: Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila
Authors: Iyer, P.P. / Lawrence, S.H. / Luther, K.B. / Rajashankar, K.R. / Yennawar, H.P. / Ferry, J.G. / Schindelin, H.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Phosphate acetyltransferase
D: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9146
Polymers70,5152
Non-polymers2,3994
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-30 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.469, 114.469, 127.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Phosphate acetyltransferase / Phosphotransacetylase


Mass: 35257.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina thermophila (archaea) / Gene: pta / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38503, phosphate acetyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.95 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: ammonium sulfate, sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 2004 / Details: doubly focusing toroidal mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 25264 / Num. obs: 23999 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 26.7
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.725 / % possible all: 91.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZT

1qzt


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 29.044 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.876 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29017 1215 5.1 %RANDOM
Rwork0.21545 ---
obs0.21915 22784 94.99 %-
all-25264 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4925 0 149 47 5121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225145
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.612.0196991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5585662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39426.111180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30815886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.981514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023681
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.22682
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23493
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4390.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.531.53382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93125302
X-RAY DIFFRACTIONr_scbond_it1.57231945
X-RAY DIFFRACTIONr_scangle_it2.4734.51689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 82 -
Rwork0.338 1700 -
obs--96.85 %
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)
14.1240.63550.01083.72550.08024.81790.04320.3284-0.3408-0.0498-0.0953-0.22060.55040.51150.0521-0.26330.0179-0.0986-0.0809-0.0489-0.552333.76828.8256-12.7277
221.4535-4.6653.544528.324616.143611.0614-1.2897-2.8853-0.98532.32361.05551.41172.44890.22630.23420.20820.0159-0.1124-0.01630.1078-0.553425.712535.03483.8637
34.1969-1.12350.5995.3619-0.94043.0681-0.4608-0.09390.850.32250.35280.0978-0.24020.1370.108-0.283-0.0336-0.2972-0.35150.0076-0.251128.061554.30536.4313
42.1542.5507-0.93364.66830.31228.4010.05180.30880.06840.045-0.2751-0.5461-0.13010.82850.2233-0.3438-0.0341-0.1126-0.12710.0183-0.469135.446638.8393-7.255
53.8876-2.1343-2.04955.72022.25888.2648-0.073-1.7940.51540.85290.11810.1885-0.74950.3401-0.04510.4254-0.0728-0.39060.6601-0.07380.83049.752387.995614.2414
614.4401-1.4598-1.53276.8157.46358.1739-0.7997-0.93151.46911.1869-0.56220.4606-1.4106-1.64511.36190.44850.0528-0.11490.2458-0.03770.83281.358674.6543.0233
74.0307-3.80361.1237.3426-1.22252.9806-0.17550.50770.7046-0.67710.06350.6136-0.1801-0.22910.112-0.1794-0.1268-0.3973-0.19210.25340.114314.873965.0043-7.689
83.38731.0428-5.246411.7552.16859.378-0.0282-0.43060.06120.41540.2851-0.6211-0.58450.875-0.25690.1248-0.0145-0.39750.00080.11510.778813.82382.27294.2372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1CA2 - 1382 - 138
2X-RAY DIFFRACTION2CA139 - 150139 - 150
3X-RAY DIFFRACTION3CA151 - 295151 - 295
4X-RAY DIFFRACTION4CA296 - 333296 - 333
5X-RAY DIFFRACTION5DB2 - 1382 - 138
6X-RAY DIFFRACTION6DB139 - 150139 - 150
7X-RAY DIFFRACTION7DB151 - 295151 - 295
8X-RAY DIFFRACTION8DB296 - 333296 - 333

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