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- PDB-3ddd: Crystal structure of A Putative Acetyltransferase (NP_142035.1) f... -

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Basic information

Entry
Database: PDB / ID: 3ddd
TitleCrystal structure of A Putative Acetyltransferase (NP_142035.1) from PYROCOCCUS HORIKOSHII at 2.25 A resolution
ComponentsPutative Acetyltransferase
KeywordsTRANSFERASE / NP_142035.1 / A Putative Acetyltransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Acetyltransferase (GNAT) family
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Aminopeptidase - #90 / YitH, acetyltransferase (GNAT) domain / : / 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 ...Aminopeptidase - #90 / YitH, acetyltransferase (GNAT) domain / : / 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 speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of A Putative Acetyltransferase (NP_142035.1) from PYROCOCCUS HORIKOSHII at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 1.5Oct 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: Putative Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7037
Polymers33,6251
Non-polymers1,0786
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.673, 113.673, 70.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative Acetyltransferase


Mass: 33624.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: NP_142035.1, PH0012 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O57768
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#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.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8M sodium citrate, 0.3M sodium chloride, 0.1M TRIS pH 7.0, 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
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 3, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→29.037 Å / Num. obs: 22597 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 38.144 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.317.30.8150.91211016480.815100
2.31-2.377.40.73511171715930.735100
2.37-2.447.30.6091.31146415610.609100
2.44-2.527.40.5281.41105614990.528100
2.52-2.67.30.4731.61069414600.473100
2.6-2.697.30.4081.91040314170.408100
2.69-2.797.30.3262.31016213840.326100
2.79-2.97.30.2543975613290.254100
2.9-3.037.30.1953.8926112700.195100
3.03-3.187.30.1494.9894012270.149100
3.18-3.357.30.1196.1848211680.119100
3.35-3.567.20.1066.4801311080.106100
3.56-3.87.20.0947.1743410350.094100
3.8-4.117.10.0827.869819780.082100
4.11-4.57.10.068963889030.068100
4.5-5.037.10.0669.458538300.066100
5.03-5.8170.0719.351697430.071100
5.81-7.126.80.0768.443226380.076100
7.12-10.066.50.0589.932965070.058100
10.06-29.045.80.0610.117252990.0696

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→29.037 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.298 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.176
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3). 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). ONE COENZYME A (COA) MONOMER WAS MODELED BASED ON THE PRESENCE OF CLEAR AND CONCLUSIVE ELECTRON DENSITY. (5). ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO SOLUTION WERE MODELED. (6). RESIDUES -5 THROUGH -11 OF THE N-TERMINAL PURIFICATION TAG ARE LOCATED IN POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1154 5.1 %RANDOM
Rwork0.168 ---
obs0.171 22552 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.366 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2---1.8 Å20 Å2
3---3.6 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 68 175 2496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222446
X-RAY DIFFRACTIONr_bond_other_d0.0020.021756
X-RAY DIFFRACTIONr_angle_refined_deg1.6352.0013301
X-RAY DIFFRACTIONr_angle_other_deg0.95734236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.61522.566113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52215438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6831525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
X-RAY DIFFRACTIONr_nbd_refined0.1990.2436
X-RAY DIFFRACTIONr_nbd_other0.2030.21862
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21163
X-RAY DIFFRACTIONr_nbtor_other0.0890.21342
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.218
X-RAY DIFFRACTIONr_mcbond_it2.03531585
X-RAY DIFFRACTIONr_mcbond_other0.4733589
X-RAY DIFFRACTIONr_mcangle_it2.89452330
X-RAY DIFFRACTIONr_scbond_it5.38481104
X-RAY DIFFRACTIONr_scangle_it6.63711971
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 86 -
Rwork0.232 1561 -
all-1647 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 29.3437 Å / Origin y: 4.7224 Å / Origin z: -0.1209 Å
111213212223313233
T-0.0831 Å20.0092 Å20.0173 Å2--0.0627 Å2-0.0316 Å2---0.0812 Å2
L0.955 °20.0521 °20.0092 °2-2.1622 °20.3372 °2--0.6468 °2
S-0.0525 Å °-0.0461 Å °-0.0518 Å °0.036 Å °-0.0001 Å °-0.042 Å °0.0176 Å °-0.0068 Å °0.0526 Å °

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