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- PDB-3shp: Crystal structure of putative acetyltransferase from Sphaerobacte... -

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Basic information

Entry
Database: PDB / ID: 3shp
TitleCrystal structure of putative acetyltransferase from Sphaerobacter thermophilus DSM 20745
ComponentsPutative acetyltransferase Sthe_0691
KeywordsTRANSFERASE / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / acetyltransferase
Function / homologyGcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / S,R MESO-TARTARIC ACID / N-acetyltransferase domain-containing protein
Function and homology information
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsChang, C. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative acetyltransferase from Sphaerobacter thermophilus DSM 20745
Authors: Chang, C. / Li, H. / Clancy, S. / Joachimiak, A.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 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: Putative acetyltransferase Sthe_0691
B: Putative acetyltransferase Sthe_0691
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9323
Polymers39,7822
Non-polymers1501
Water4,648258
1
A: Putative acetyltransferase Sthe_0691
B: Putative acetyltransferase Sthe_0691
hetero molecules

A: Putative acetyltransferase Sthe_0691
B: Putative acetyltransferase Sthe_0691
hetero molecules

A: Putative acetyltransferase Sthe_0691
B: Putative acetyltransferase Sthe_0691
hetero molecules

A: Putative acetyltransferase Sthe_0691
B: Putative acetyltransferase Sthe_0691
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,72912
Polymers159,1288
Non-polymers6004
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area23230 Å2
ΔGint-53 kcal/mol
Surface area54330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.196, 89.196, 115.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Putative acetyltransferase Sthe_0691


Mass: 19891.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / S 6022 / Gene: Sthe_0691 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1C1L1
#2: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M di-ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 24095 / Num. obs: 24074 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 40.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 6.35 / Num. unique all: 1180 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.988 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1221 5.1 %RANDOM
Rwork0.189 ---
all0.1912 23952 --
obs0.1912 23952 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 106.37 Å2 / Biso mean: 38.2712 Å2 / Biso min: 13.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 10 258 2827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222686
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9383657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54422.283127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88815426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5641529
X-RAY DIFFRACTIONr_chiral_restr0.0890.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212064
X-RAY DIFFRACTIONr_mcbond_it1.461.51665
X-RAY DIFFRACTIONr_mcangle_it2.67822649
X-RAY DIFFRACTIONr_scbond_it3.11331021
X-RAY DIFFRACTIONr_scangle_it4.9654.51008
X-RAY DIFFRACTIONr_rigid_bond_restr1.66432686
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 68 -
Rwork0.186 1524 -
all-1592 -
obs-1592 90.45 %
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)
10.16560.040.05250.0562-0.02750.1777-0.0053-0.0030.00990.0042-0.0019-0.0028-0.0022-0.00520.00720.0054-0.00130.0030.01230.0020.005526.275729.964118.8495
20.2204-0.053-0.08140.0840.03250.1125-0.0085-0.0006-0.02230.01630.003300.0076-0.00870.00530.0164-0.00270.0010.00990.00230.003627.803318.99087.8866
30.36570.1001-0.00790.3150.03550.11850.00820.00060.0041-0.0320.0026-0.0128-0.0135-0.0001-0.01080.01580.00260.00540.0113-0.00320.003730.060159.948118.0976
40.1246-0.0526-0.07330.206-0.00370.45750.00660.00550.0010.0177-0.0041-0.0028-0.0465-0.0222-0.00250.01220.00090.00120.0078-0.00370.002422.649954.2284.6474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 116
2X-RAY DIFFRACTION2A117 - 168
3X-RAY DIFFRACTION3B1 - 116
4X-RAY DIFFRACTION4B117 - 165

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