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- PDB-3k9u: Crystal structure of paia acetyltransferase (ta0374) from thermop... -

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Basic information

Entry
Database: PDB / ID: 3k9u
TitleCrystal structure of paia acetyltransferase (ta0374) from thermoplasma acidophilum
ComponentsPaiA Acetyltransferase
KeywordsTRANSFERASE / THERMOPLASMA ACIDOPHILUM / ACETYLTRANSFERASE / 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
ACETYL COENZYME *A / BROMIDE ION / NICKEL (II) ION / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / 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
DepositionOct 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 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 1.4Sep 6, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_asym_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: PaiA Acetyltransferase
B: PaiA Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4829
Polymers37,6182
Non-polymers1,8647
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-52 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.280, 70.577, 87.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 6 / Auth seq-ID: 1 - 159 / Label seq-ID: 1 - 159

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsBIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A, B, G, H, L, C, F BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PaiA Acetyltransferase


Mass: 18808.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0374 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21magic / References: UniProt: Q9HL57

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Non-polymers , 5 types, 82 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium Bromide, 20% PEG 3350, 0.1 M Bis-Tris propane, 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-G / Wavelength: 0.97872 Å
DetectorDetector: CCD / Date: Mar 16, 2009 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→54.98 Å / Num. all: 19708 / Num. obs: 19708 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 17.469
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 10.2 / Rsym value: 0.185 / % possible all: 98.6

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
MOLREPphasing
REFMAC5.5.0051refinement
HKL-2000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F0A

3f0a


Resolution: 2.3→54.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.592 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1001 5.1 %RANDOM
Rwork0.191 ---
obs0.194 19697 98.57 %-
all-19697 --
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 mean: 21.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--1.25 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→54.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 107 75 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222815
X-RAY DIFFRACTIONr_bond_other_d0.0010.021977
X-RAY DIFFRACTIONr_angle_refined_deg1.4722.0223791
X-RAY DIFFRACTIONr_angle_other_deg0.85834822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36224.146123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80215556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8851514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
X-RAY DIFFRACTIONr_mcbond_it0.9011.51585
X-RAY DIFFRACTIONr_mcbond_other0.2351.5649
X-RAY DIFFRACTIONr_mcangle_it1.74622554
X-RAY DIFFRACTIONr_scbond_it2.85531230
X-RAY DIFFRACTIONr_scangle_it4.5514.51236
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2278 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.75
Bloose thermal2.4310
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 78 -
Rwork0.192 1361 -
obs--98.63 %
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)
12.6662-0.2011-0.51311.71680.14170.91070.01490.03590.1342-0.0506-0.05960.064-0.082-0.12270.04470.01330.01170.00280.0267-0.0250.071312.275-16.789-5.286
21.825-0.1524-0.0762.9756-0.09742.05230.00310.0527-0.117-0.0102-0.0103-0.20150.30360.11310.00730.09180.02370.00920.0285-0.0410.102635.071-40.044-16.584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 159
2X-RAY DIFFRACTION2B1 - 159

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