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- PDB-3owc: Crystal structure of GNAT superfamily protein PA2578 from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 3owc
TitleCrystal structure of GNAT superfamily protein PA2578 from Pseudomonas aeruginosa
ComponentsProbable acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Acyl-CoA N-acyltransferase (Nat) / GNAT / acetyltransferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl 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
COENZYME A / Acetyltransferase PA2578
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMajorek, K.A. / Chruszcz, M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of GNAT superfamily protein PA2578 from Pseudomonas aeruginosa
Authors: Majorek, K.A. / Chruszcz, M. / Joachimiak, A. / Minor, W.
History
DepositionSep 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 26, 2012Group: Structure summary
Revision 1.3Dec 19, 2012Group: Structure summary
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Probable acetyltransferase
B: Probable acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7339
Polymers42,8882
Non-polymers1,8457
Water4,234235
1
A: Probable acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3985
Polymers21,4441
Non-polymers9544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3364
Polymers21,4441
Non-polymers8923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.095, 71.095, 97.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Probable acetyltransferase


Mass: 21443.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2578 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9I0Q8
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / 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.: 235 / 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: 57.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% Tacsimate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 18, 2010 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 38282 / Num. obs: 38282 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 27
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.526 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000SOLVE/RESOLVEphasing
SHELXDphasing
SHELXEmodel building
BUCCANEERphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.889 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21214 1915 5 %RANDOM
Rwork0.17649 ---
obs0.17829 36345 99.77 %-
all-38260 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.104 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 116 235 3108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213156
X-RAY DIFFRACTIONr_bond_other_d0.0010.022224
X-RAY DIFFRACTIONr_angle_refined_deg2.0472.034310
X-RAY DIFFRACTIONr_angle_other_deg2.22335300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45221.242153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07115497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3951548
X-RAY DIFFRACTIONr_chiral_restr0.1310.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213470
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02734
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_it1.0281.51771
X-RAY DIFFRACTIONr_mcbond_other0.1781.5714
X-RAY DIFFRACTIONr_mcangle_it1.74222827
X-RAY DIFFRACTIONr_scbond_it2.96631385
X-RAY DIFFRACTIONr_scangle_it4.4874.51483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 145 -
Rwork0.246 2674 -
obs--99.86 %
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)
14.87820.06291.68531.6007-0.53632.7430.27440.4015-0.4153-0.0521-0.15430.00290.3320.4468-0.12020.05040.0654-0.04140.2907-0.03450.290631.9132.12729.604
21.9026-0.26230.76630.9628-0.1431.22480.0071-0.13020.12650.085-0.0485-0.2804-0.08560.32570.04140.0306-0.0247-0.01830.1962-0.03450.207124.30812.63631.883
37.18471.1692.15793.7058-0.31662.0140.0243-0.33330.41450.25490.0324-0.077-0.35830.2076-0.05670.1439-0.02080.01320.1756-0.05170.192913.84215.43932.787
42.25971.08811.21084.40942.24743.4663-0.0414-0.12370.08170.02920.0042-0.111-0.04310.11550.03720.0940.01610.00510.1601-0.00970.183714.08710.26227.365
51.29150.4775-0.16434.5201-0.29811.91560.0240.14560.1034-1.14860.0458-0.3515-0.2709-0.0214-0.06980.43410.03290.13260.037-0.01690.158212.40113.0530.897
61.5118-0.2669-0.16412.8345-0.97131.54170.08860.04650.1412-0.1342-0.05160.1817-0.2616-0.0451-0.0370.13470.02070.02670.06820.00040.18437.08516.87415.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 76
2X-RAY DIFFRACTION2A77 - 143
3X-RAY DIFFRACTION3A144 - 155
4X-RAY DIFFRACTION4A156 - 180
5X-RAY DIFFRACTION5B11 - 126
6X-RAY DIFFRACTION6B127 - 180

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