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- PDB-3fix: Crystal structure of a putative n-acetyltransferase (ta0374) from... -

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Basic information

Entry
Database: PDB / ID: 3fix
TitleCrystal structure of a putative n-acetyltransferase (ta0374) from thermoplasma acidophilum
ComponentsN-ACETYLTRANSFERASE
KeywordsTRANSFERASE / N-ACETYLTRANSFERASE / TERMOPLASMA ACIDOPHILUM / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


negative regulation of sporulation / diamine N-acetyltransferase / diamine N-acetyltransferase activity
Similarity search - Function
: / 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
Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of the novel PaiA N-acetyltransferase from Thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production.
Authors: Filippova, E.V. / Shuvalova, L. / Minasov, G. / Kiryukhina, O. / Zhang, Y. / Clancy, S. / Radhakrishnan, I. / Joachimiak, A. / Anderson, W.F.
History
DepositionDec 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: N-ACETYLTRANSFERASE
B: N-ACETYLTRANSFERASE
C: N-ACETYLTRANSFERASE
D: N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0856
Polymers86,9614
Non-polymers1242
Water70339
1
A: N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8022
Polymers21,7401
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)21,7401
Polymers21,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8022
Polymers21,7401
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)21,7401
Polymers21,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: N-ACETYLTRANSFERASE
B: N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5433
Polymers43,4812
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
C: N-ACETYLTRANSFERASE
D: N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5433
Polymers43,4812
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.229, 60.915, 72.116
Angle α, β, γ (deg.)101.19, 90.10, 89.97
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA-5 - 15919 - 183
21TYRTYRCC-5 - 15919 - 183
12ILEILEBB3 - 15927 - 183
22ILEILEDD3 - 15927 - 183

NCS ensembles :
ID
1
2

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Components

#1: Protein
N-ACETYLTRANSFERASE


Mass: 21740.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0374 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q9HL57
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 10% (w/v) PEG 8000, 10% (w/v) ETHYLENE GLYCOL , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorDetector: CCD / Date: Aug 11, 2008 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 30257 / Num. obs: 30257 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 67.6 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / % possible all: 91.2

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0051refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 21.946 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27555 1530 5.1 %RANDOM
Rwork0.22972 ---
obs0.23215 28727 97.15 %-
all-28727 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.231 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20.11 Å20.02 Å2
2---4.89 Å2-1.98 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5331 0 8 39 5378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225445
X-RAY DIFFRACTIONr_bond_other_d0.0030.023857
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9777304
X-RAY DIFFRACTIONr_angle_other_deg1.16639402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0435642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48624.146246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.604151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1921528
X-RAY DIFFRACTIONr_chiral_restr0.120.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025856
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021128
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9541.53198
X-RAY DIFFRACTIONr_mcbond_other0.2361.51314
X-RAY DIFFRACTIONr_mcangle_it1.79325151
X-RAY DIFFRACTIONr_scbond_it3.02632247
X-RAY DIFFRACTIONr_scangle_it4.9154.52153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2346TIGHT POSITIONAL0.020.05
1A2346TIGHT THERMAL0.10.5
2B2230TIGHT POSITIONAL0.030.05
2B2230TIGHT THERMAL0.070.5
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 96 -
Rwork0.336 1983 -
obs--90.75 %
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)
12.8480.57060.53063.9811-0.18172.40330.0492-0.02850.111-0.2178-0.01930.0572-0.10380.1679-0.02990.0296-0.023-0.00760.042-0.00190.0541-9.3885-12.1738-5.6269
24.3035-1.5373-0.91854.76870.61753.039-0.1646-0.53090.2770.66670.3402-0.1915-0.10830.3213-0.17570.24960.0003-0.02370.1528-0.06230.03-23.9344-18.320524.908
32.6219-0.8199-0.39323.9836-0.24852.29570.01070.0538-0.13680.22090.00970.0540.12370.181-0.02040.02650.02080.00580.037-0.00370.0622-30.5428-48.30033.9133
44.47481.45640.84914.64240.85413.0581-0.17920.553-0.2954-0.59820.32-0.24260.08270.2932-0.14070.233-0.00620.01680.1464-0.06140.0303-44.9696-42.1676-26.6037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 159
2X-RAY DIFFRACTION2B3 - 159
3X-RAY DIFFRACTION3C-5 - 159
4X-RAY DIFFRACTION4D3 - 159

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