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- PDB-2oh1: Crystal structure of acetyltransferase GNAT family (YP_013287.1) ... -

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Basic information

Entry
Database: PDB / ID: 2oh1
TitleCrystal structure of acetyltransferase GNAT family (YP_013287.1) from Listeria monocytogenes 4b F2365 at 1.46 A resolution
ComponentsAcetyltransferase, GNAT family
KeywordsTRANSFERASE / YP_013287.1 / acetyltransferase GNAT family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyGcn5-related N-acetyltransferase (GNAT) / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / Unknown ligand / :
Function and homology information
Biological speciesListeria monocytogenes str. 4b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.46 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of acetyltransferase GNAT family (YP_013287.1) from Listeria monocytogenes 4b F2365 at 1.46 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Remark 300 BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE STATIC LIGHT SCATTERING WITH ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY MEASUREMENTS INDICATE THAT THE MONOMER IS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (SEQUENCE NUMBER 0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase, GNAT family
B: Acetyltransferase, GNAT family
C: Acetyltransferase, GNAT family
D: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,97314
Polymers83,5394
Non-polymers43410
Water15,097838
1
A: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0094
Polymers20,8851
Non-polymers1243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9473
Polymers20,8851
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0714
Polymers20,8851
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9473
Polymers20,8851
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.624, 99.833, 122.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Acetyltransferase, GNAT family


Mass: 20884.744 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes str. 4b (bacteria)
Species: Listeria monocytogenes / Strain: F2365 / Gene: YP_013287.1, LMOf2365_0683 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q722P7, Transferases; Acyltransferases
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 277 K / pH: 7
Details: NANODROP, 1.0M Na Citrate, 0.2M NaCl, 0.1M TRIS pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97932, 0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2006 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT (HORIZONTAL FOCUSING)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.979011
ReflectionResolution: 1.46→46.225 Å / Num. obs: 125870 / % possible obs: 89.6 % / Biso Wilson estimate: 25.14 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.54
Reflection shellResolution: 1.46→1.51 Å / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 1.79 / % possible all: 52.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.46→46.225 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.672 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.071
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. UNIDENTIFIED ELECTRON DENSITY FOUND NEAR THE ACTIVE SITE WAS MODELED AS AN UNKNOWN LIGAND (UNL). 5. THE ELECTRON DENSITIES SHOW THAT RESIDUES SER42 AND THR43 IN SUBUNIT A ARE DISORDERED, AND THESE RESIDUES WERE MODELED BASED ON THE MODEL FOR THE NCS-RELATED B SUBUNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 6317 5 %RANDOM
Rwork0.168 ---
all0.17 ---
obs0.17 125813 89.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--0.64 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.46→46.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5509 0 52 838 6399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226098
X-RAY DIFFRACTIONr_bond_other_d0.0010.024111
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9468296
X-RAY DIFFRACTIONr_angle_other_deg0.963310009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7095788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13823.705278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.564151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2751539
X-RAY DIFFRACTIONr_chiral_restr0.0970.2899
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027031
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021348
X-RAY DIFFRACTIONr_nbd_refined0.2620.21267
X-RAY DIFFRACTIONr_nbd_other0.2050.24571
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23107
X-RAY DIFFRACTIONr_nbtor_other0.0870.23225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2662
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.233
X-RAY DIFFRACTIONr_mcbond_it2.3533910
X-RAY DIFFRACTIONr_mcbond_other0.57531521
X-RAY DIFFRACTIONr_mcangle_it3.2356043
X-RAY DIFFRACTIONr_scbond_it5.20982619
X-RAY DIFFRACTIONr_scangle_it6.786112253
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 264 -
Rwork0.279 4952 -
obs-5216 50.9 %
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)
10.26730.14650.32570.78510.03880.8807-0.01130.04270.0329-0.03670.03390.0878-0.0223-0.0181-0.0226-0.0562-0.00760.0154-0.01590.0076-0.005422.830741.56622.4147
20.79160.4089-0.00621.23010.0520.30890.0977-0.1858-0.08630.2618-0.1097-0.01930.06770.07870.0120.0055-0.0190.01110.01630.0309-0.023334.062226.065721.7705
31.0003-0.3944-0.15980.33720.1010.50940.0630.16990.1182-0.1196-0.0061-0.0339-0.10430.0051-0.0569-0.0092-0.01370.0109-0.030.0143-0.027255.448765.58193.3146
40.73880.0009-0.11760.3461-0.06610.8097-0.0046-0.12610.01240.09680.0298-0.0223-0.00370.0906-0.0252-0.02020.0051-0.0047-0.0095-0.0231-0.033259.990556.221928.248
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 1785 - 179
22BB3 - 1764 - 177
33CC4 - 1755 - 176
44DD3 - 1764 - 177

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