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- PDB-1vmi: Crystal structure of Putative phosphate acetyltransferase (np_416... -

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Basic information

Entry
Database: PDB / ID: 1vmi
TitleCrystal structure of Putative phosphate acetyltransferase (np_416953.1) from Escherichia coli k12 at 2.32 A resolution
Componentsputative phosphate acetyltransferase
KeywordsTRANSFERASE / np_416953.1 / Putative phosphate acetyltransferase / structural genomics / JCSG / protein structure initiative / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


phosphate acetyltransferase activity / phosphate acetyltransferase / ethanolamine catabolic process / response to heat
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphate acetyltransferase EutD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.32 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative phosphate acetyltransferase (np_416953.1) from Escherichia coli k12 at 2.32 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE CLONING ARTIFACT: RESIDUE 1 OF THE GENE IS NOT INCLUDED IN THE CONSTRUCT. THE CONSTRUCT ...SEQUENCE CLONING ARTIFACT: RESIDUE 1 OF THE GENE IS NOT INCLUDED IN THE CONSTRUCT. THE CONSTRUCT HAS THE 13 AMINO ACID N-TERMINAL TAG FOLLOWED BY RESIDUES 2-338 OF THE EC5317A GENE PRODUCT AND A 5 AMINO ACID C-TERMINAL TAG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5733
Polymers38,3891
Non-polymers1842
Water1,63991
1
A: putative phosphate acetyltransferase
hetero molecules

A: putative phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1466
Polymers76,7782
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area3830 Å2
ΔGint-26 kcal/mol
Surface area25790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.307, 95.307, 175.512
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

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Components

#1: Protein putative phosphate acetyltransferase


Mass: 38388.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eutD, eutI / Production host: Escherichia coli (E. coli) / References: UniProt: P77218, phosphate acetyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.29 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.5
Details: 1.26M (NH4)2SO4, 0.2M NaCl, 0.1M CHES pH 9.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.110.9796
SYNCHROTRONALS 8.2.120.9796, 0.9794, 1.0000
DetectorType: ADSC / Detector: CCD / Date: Aug 24, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97941
311
ReflectionResolution: 2.32→28.26 Å / Num. obs: 21138 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 60.11 Å2 / Rsym value: 0.062 / Net I/σ(I): 13.3
Reflection shellResolution: 2.32→2.45 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3011 / Rsym value: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHELXmodel building
autoSHARPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.32→28.26 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 14.07 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24746 1085 5.1 %RANDOM
Rwork0.19419 ---
obs0.1968 20017 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.266 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.32→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 12 91 2500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222454
X-RAY DIFFRACTIONr_bond_other_d0.0010.022344
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9813341
X-RAY DIFFRACTIONr_angle_other_deg0.85535414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7345328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58523.70889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01115377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2431517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02461
X-RAY DIFFRACTIONr_nbd_refined0.2110.2519
X-RAY DIFFRACTIONr_nbd_other0.1750.22293
X-RAY DIFFRACTIONr_nbtor_other0.0890.21537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.27
X-RAY DIFFRACTIONr_mcbond_it0.9211.51697
X-RAY DIFFRACTIONr_mcbond_other0.1671.5659
X-RAY DIFFRACTIONr_mcangle_it1.1722621
X-RAY DIFFRACTIONr_scbond_it2.4773852
X-RAY DIFFRACTIONr_scangle_it3.6094.5720
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21215
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 88 5.76 %
Rwork0.274 1441 -
obs--99.93 %
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)
13.37652.45440.50613.5750.5843.00970.07090.12520.2968-0.104-0.09910.1354-0.54290.17050.0281-0.0743-0.00410.0305-0.1729-0.0557-0.1033-3.134739.968912.6246
23.2030.69620.64922.363.06634.00560.08360.2577-0.5742-0.05160.1969-0.35460.29970.2087-0.2804-0.08740.03380.001-0.0932-0.09160.0479-0.253720.262110.5063
33.70331.751-0.42789.4125-1.13255.25470.04220.25410.1970.0692-0.0037-0.1295-0.11490.3983-0.0386-0.07270.0197-0.0796-0.0597-0.0273-0.1377.768629.927231.999
43.26230.6623-0.48562.20611.5933.7608-0.06430.0014-0.08540.05050.1969-0.54140.26171.2273-0.1327-0.04150.0923-0.11780.2223-0.04960.041515.128326.767942.849
50.8056-0.61051.40410.6815-1.71794.40080.03780.149-0.0603-0.00130.0567-0.1051-0.13560.0271-0.0945-0.0861-0.0647-0.0158-0.1175-0.0605-0.0758-1.013933.801127.9864
Refinement TLS group

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

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11-6 - 707 - 82
2271 - 14783 - 159
33148 - 195160 - 207
44196 - 268208 - 280
55269 - 323281 - 335

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