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- PDB-3s6f: Crystal structure of a putative acetyltransferase (DR_1678) from ... -

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Basic information

Entry
Database: PDB / ID: 3s6f
TitleCrystal structure of a putative acetyltransferase (DR_1678) from Deinococcus radiodurans R1 at 1.19 A resolution
ComponentsHypothetical acetyltransferase
KeywordsTRANSFERASE / Acyl-CoA N-acyltransferases / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


N-acetyltransferase activity / metal ion binding
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
COENZYME A / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.19 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of a Hypothetical acetyltransferase (DR_1678) from Deinococcus radiodurans at 1.19 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0164
Polymers16,1691
Non-polymers8483
Water4,252236
1
A: Hypothetical acetyltransferase
hetero molecules

A: Hypothetical acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0338
Polymers32,3382
Non-polymers1,6956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area6980 Å2
ΔGint-53 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.168, 102.524, 51.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-369-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Hypothetical acetyltransferase


Mass: 16168.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_1678 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9RTS8
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Ca(OAc)2, 10.0% PEG-8000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97944,0.97916
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2007
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979441
30.979161
ReflectionResolution: 1.19→39.253 Å / Num. obs: 63440 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 9.484 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsRsym value% possible all
1.19-1.223.60.5252.51676046230.52598
1.22-1.253.60.452.91611844480.4598.1
1.25-1.293.60.4073.21596143850.40798.5
1.29-1.333.60.333.91539842340.3398.6
1.33-1.373.60.2834.61500441210.28398.7
1.37-1.423.60.2465.31462240110.24699
1.42-1.483.70.1946.71427539090.19499.1
1.48-1.543.60.1568.51354537110.15699.5
1.54-1.63.60.119111323036270.11999.8
1.6-1.683.70.10113.21255334380.10199.7
1.68-1.773.60.08615.71207433130.08699.9
1.77-1.883.60.065211137431210.06599.6
1.88-2.013.60.051271073029460.05199.9
2.01-2.173.60.04232.91000527540.04299.9
2.17-2.383.60.03937917025340.03999.8
2.38-2.663.60.03641824523020.03699.9
2.66-3.073.60.03444.5725120410.03499.8
3.07-3.763.60.02851.1628917670.02899.9
3.76-5.323.50.02654.3474213660.02699.5
5.32-39.2533.20.03151.625127890.03198.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJune 12data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.19→39.253 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.32 / SU B: 0.894 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.03
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. COENZYME A (COA) HAS BEEN MODELED BASED ON DENSITY. 5. THERE IS SOME UNMODELED DENSITY NEAR COA SUGGESTING THE PRESENCE OF A SMALL MOLECULE LIGAND.
RfactorNum. reflection% reflectionSelection details
Rfree0.1504 3215 5.1 %RANDOM
Rwork0.1351 ---
obs0.1358 63421 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.83 Å2 / Biso mean: 16.7661 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.19→39.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1111 0 50 236 1397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221379
X-RAY DIFFRACTIONr_bond_other_d0.0010.02929
X-RAY DIFFRACTIONr_angle_refined_deg1.8332.0581915
X-RAY DIFFRACTIONr_angle_other_deg1.0432263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3945176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07822.74262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54515214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3761516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211538
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02285
X-RAY DIFFRACTIONr_mcbond_it1.6531.5792
X-RAY DIFFRACTIONr_mcbond_other0.821.5318
X-RAY DIFFRACTIONr_mcangle_it2.47121293
X-RAY DIFFRACTIONr_scbond_it3.3443587
X-RAY DIFFRACTIONr_scangle_it4.7554.5612
X-RAY DIFFRACTIONr_rigid_bond_restr1.59132308
X-RAY DIFFRACTIONr_sphericity_free9.9353255
X-RAY DIFFRACTIONr_sphericity_bonded4.69132262
LS refinement shellResolution: 1.19→1.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 238 -
Rwork0.22 4381 -
all-4619 -
obs--97.8 %

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