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- PDB-3c26: Crystal structure of a putative acetyltransferase (NP_394282.1) f... -

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Basic information

Entry
Database: PDB / ID: 3c26
TitleCrystal structure of a putative acetyltransferase (NP_394282.1) from Thermoplasma acidophilum at 2.00 A resolution
ComponentsPutative acetyltransferase Ta0821
KeywordsTRANSFERASE / NP_394282.1 / A Putative Acetyltransferase / Acetyltransferase (GNAT) family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
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
NITRATE ION / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative acetyltransferase (NP_394282.1) from Thermoplasma acidophilum at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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

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Assembly

Deposited unit
A: Putative acetyltransferase Ta0821
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4869
Polymers30,9901
Non-polymers4968
Water2,702150
1
A: Putative acetyltransferase Ta0821
hetero molecules

A: Putative acetyltransferase Ta0821
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,97218
Polymers61,9792
Non-polymers99316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.820, 86.820, 67.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative acetyltransferase Ta0821


Mass: 30989.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Species: Thermoplasma acidophilum / Strain: DSM 1728 / AMRC-C165 / IFO 15155 / JCM 9062 / Gene: NP_394282.1, Ta0821 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HJZ0
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: NANODROP, 0.2M NaNO3, 20.0% PEG 3350, No Buffer pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97895 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 9, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2→29.488 Å / Num. obs: 17927 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.54 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.53
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.62.2120663221199.1
2.07-2.150.5112.61223831981100
2.15-2.250.4263.1130383410199.9
2.25-2.370.3433.81285433531100
2.37-2.520.2884.6128603345199.9
2.52-2.710.2226.1126373284199.9
2.71-2.990.158.81317234121100
2.99-3.420.08115.31274232861100
3.42-4.30.04525.4127463296199.9
4.3-29.4880.03233.1127053338198.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.488 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.552 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.18
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. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. THERE IS AN UNKNOWN DENSITY NEAR HIS 140. 5. NO3 AND EDO WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 912 5.1 %RANDOM
Rwork0.179 ---
obs0.182 17882 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.439 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→29.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 32 150 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222159
X-RAY DIFFRACTIONr_bond_other_d0.0010.021476
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.952920
X-RAY DIFFRACTIONr_angle_other_deg1.2883.0013544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4195259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46622.816103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23215340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8071516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022411
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02487
X-RAY DIFFRACTIONr_mcbond_it0.8941.51289
X-RAY DIFFRACTIONr_mcbond_other0.2171.5525
X-RAY DIFFRACTIONr_mcangle_it1.60622065
X-RAY DIFFRACTIONr_scbond_it2.5853870
X-RAY DIFFRACTIONr_scangle_it4.0374.5853
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 79 -
Rwork0.211 1193 -
all-1272 -
obs--99.22 %
Refinement TLS params.Method: refined / Origin x: 32.647 Å / Origin y: 29.627 Å / Origin z: 17.476 Å
111213212223313233
T-0.0471 Å2-0.0206 Å20.0005 Å2--0.0161 Å20.0021 Å2---0.0974 Å2
L0.719 °2-0.0694 °2-0.0155 °2-1.0069 °2-0.1242 °2--0.6665 °2
S-0.0146 Å °0.0539 Å °0.0245 Å °-0.0092 Å °0.0031 Å °0.0347 Å °0.0321 Å °-0.0636 Å °0.0115 Å °

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