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- PDB-2ge3: Crystal structure of Probable acetyltransferase from Agrobacteriu... -

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Basic information

Entry
Database: PDB / ID: 2ge3
TitleCrystal structure of Probable acetyltransferase from Agrobacterium tumefaciens
Componentsprobable acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / Agrobacterium tumefaciens / Structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Probable acetyltransferase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsChang, C. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Probable acetyltransferase from Agrobacterium tumefaciens
Authors: Chang, C. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMar 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: probable acetyltransferase
B: probable acetyltransferase
C: probable acetyltransferase
D: probable acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7497
Polymers77,3214
Non-polymers2,4293
Water6,756375
1
A: probable acetyltransferase
B: probable acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2804
Polymers38,6602
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-8 kcal/mol
Surface area15380 Å2
MethodPISA
2
C: probable acetyltransferase
D: probable acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4703
Polymers38,6602
Non-polymers8101
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-9 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.906, 90.796, 103.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
probable acetyltransferase


Mass: 19330.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UD38, UniProt: A9CI25*PLUS
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M Sodium/Potassium Phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 36530 / Num. obs: 36493 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 35.94
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.04 / Num. unique all: 3609 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.066 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26079 1814 5 %RANDOM
Rwork0.18978 ---
all0.19353 34493 --
obs0.19353 34493 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5147 0 153 375 5675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0215410
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2991.9747326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14821.667264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32915872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4291568
X-RAY DIFFRACTIONr_chiral_restr0.1420.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024121
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2560.22539
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23586
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2362
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6121.53391
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18125174
X-RAY DIFFRACTIONr_scbond_it3.82132304
X-RAY DIFFRACTIONr_scangle_it5.4584.52152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 126 -
Rwork0.224 2418 -
obs--95.39 %
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)
10.08860.48340.08112.63720.44511.66250.07150.05040.0743-0.0094-0.20130.35030.1474-0.24640.12980.0018-0.03470.0067-0.0035-0.0118-0.106131.14342.6877.656
20.3646-0.45880.0431.76621.14731.2190.1261-0.0429-0.04690.1024-0.0160.08190.20460.1091-0.11010.0866-0.00170.0076-0.02690.0082-0.094941.61743.50521.172
31.3725-0.6117-1.01583.50950.04851.30810.06220.0397-0.0179-0.0544-0.02670.4111-0.0699-0.2353-0.0354-0.03110.03510.0408-0.07270.0369-0.099122.7660.31835.938
41.365-0.7129-0.66241.20690.89250.67930.0522-0.05350.1383-0.00820.0512-0.0885-0.12810.2101-0.10340.0831-0.01660.0194-0.08420.0028-0.064838.87558.83431.179
51.5120.28760.76311.7758-1.34222.28030.1785-0.0528-0.2413-0.07920.17790.11560.30910.0642-0.35640.0623-0.0047-0.0992-0.09130.0079-0.14112.44583.07510.059
61.38350.68421.16743.32760.58880.9850.2198-0.3828-0.09390.2306-0.065-0.0460.10790.2244-0.15480.0299-0.0335-0.06380.06150.0091-0.133624.46788.59420.516
73.3616-1.7591-0.59943.617-1.45322.08720.3793-0.180.37990.10440.04170.5801-0.27470.0138-0.421-0.0402-0.13220.23840.0101-0.20750.09568.332112.47726.055
82.2462-0.160.41583.64892.4381.75090.0669-0.31220.5139-0.43470.060.1918-0.62590.4754-0.12690.0118-0.14130.04350.0235-0.145-0.036824.069107.06621.975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1206 - 120
2X-RAY DIFFRACTION2AA121 - 169121 - 169
3X-RAY DIFFRACTION3BB7 - 1207 - 120
4X-RAY DIFFRACTION4BB121 - 169121 - 169
5X-RAY DIFFRACTION5CC6 - 1206 - 120
6X-RAY DIFFRACTION6CC121 - 169121 - 169
7X-RAY DIFFRACTION7DD7 - 1207 - 120
8X-RAY DIFFRACTION8DD121 - 169121 - 169

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