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- PDB-2il4: Crystal structure of At1g77540-Coenzyme A Complex -

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Basic information

Entry
Database: PDB / ID: 2il4
TitleCrystal structure of At1g77540-Coenzyme A Complex
ComponentsProtein At1g77540
KeywordsTRANSFERASE / CoA / Coenzyme-A / COG2388 Family / acetyltransferase / At1g77540 / STRUCTURAL GENOMICS FUNCTIONAL FOLLOW-UP STUDY / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


histone acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peroxisome
Similarity search - Function
Gcn5-related N-acetyltransferase / Yjdj-type Gcn5-related N-acetyltransferase / GCN5-related N-acetyl-transferase / Yjdj-type Gcn5-related N-acetyltransferase (GNAT) domain profile. / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acetyltransferase At1g77540
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsBitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Biochemistry / Year: 2006
Title: Structure of Arabidopsis thaliana At1g77540 Protein, a Minimal Acetyltransferase from the COG2388 Family.
Authors: Tyler, R.C. / Bitto, E. / Berndsen, C.E. / Bingman, C.A. / Singh, S. / Lee, M.S. / Wesenberg, G.E. / Denu, J.M. / Phillips, G.N. / Markley, J.L.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionOct 17, 2006ID: 2GDB
Revision 1.0Oct 17, 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 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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

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Assembly

Deposited unit
A: Protein At1g77540
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5202
Polymers11,7521
Non-polymers7681
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.905, 63.941, 29.525
Angle α, β, γ (deg.)90.000, 90.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein At1g77540


Mass: 11752.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g77540 / Plasmid: PVP13-GW / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) PLACI+RARE / References: UniProt: Q9CAQ2
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (29% PEG 5000, 0.10 M SODIUM ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (29% PEG 5000, 0.10 M SODIUM CITRATE, 0.10 M PIPES PH 6.5). CRYSTALS SOAKED 16 HOURS IN WELL SOLUTION SUPPLEMENTED WITH 0.009 M acetyl-Coenzyme. Crystals cryo-protected with fomblin 2500, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2005
Details: Double crystal monochromator, Si111, 2nd crystal sagital focus followed by Rh coated bent cylinder vertically focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.05→31.98 Å / Num. obs: 6473 / % possible obs: 99.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.052 / Χ2: 0.993 / Net I/σ(I): 18.303
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 4.993 / Num. unique all: 432 / Χ2: 0.902 / % possible all: 98

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Phasing

Phasing MRRfactor: 0.462 / Cor.coef. Fo:Fc: 0.533
Highest resolutionLowest resolution
Rotation2.1 Å31.97 Å
Translation2.1 Å31.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XMT

1xmt


Resolution: 2.054→31.976 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.16 / SU B: 8.596 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 636 9.848 %RANDOM
Rwork0.16 ---
obs0.166 6458 99.095 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 33.963 Å2
Baniso -1Baniso -2Baniso -3
1-0.716 Å20 Å22.045 Å2
2---0.701 Å20 Å2
3---0.046 Å2
Refinement stepCycle: LAST / Resolution: 2.054→31.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 0 48 61 837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022813
X-RAY DIFFRACTIONr_angle_refined_deg1.6642.0031107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.958591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.24122.35334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08415126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.802155
X-RAY DIFFRACTIONr_chiral_restr0.1110.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02605
X-RAY DIFFRACTIONr_nbd_refined0.2070.2371
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.27
X-RAY DIFFRACTIONr_mcbond_it1.6082465
X-RAY DIFFRACTIONr_mcangle_it2.6214738
X-RAY DIFFRACTIONr_scbond_it4.8826392
X-RAY DIFFRACTIONr_scangle_it6.5148368
LS refinement shellResolution: 2.054→2.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 39 -
Rwork0.18 419 -
all-474 -
obs--96.624 %
Refinement TLS params.Method: refined / Origin x: 1.8965 Å / Origin y: 0.2197 Å / Origin z: 3.6025 Å
111213212223313233
T-0.1145 Å2-0.01 Å20.0029 Å2--0.1183 Å20.0095 Å2---0.1085 Å2
L2.7878 °2-0.5311 °20.4441 °2-3.1089 °2-0.8882 °2--3.4672 °2
S0.0357 Å °-0.0451 Å °-0.0978 Å °0.1331 Å °0.0866 Å °0.0418 Å °-0.1296 Å °-0.0907 Å °-0.1223 Å °
Refinement TLS groupSelection: ALL

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