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- PDB-5ib0: PA4534: acetyl CoA complex -

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Basic information

Entry
Database: PDB / ID: 5ib0
TitlePA4534: acetyl CoA complex
ComponentsUncharacterized protein PA4534
KeywordsTRANSFERASE / Acetyl transferase
Function / homology
Function and homology information


N-acetyltransferase activity / 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
ACETYL COENZYME *A / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsChoe, J. / Shin, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of PA4534
Authors: Choe, J. / Shin, S.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein PA4534
B: Uncharacterized protein PA4534
C: Uncharacterized protein PA4534
D: Uncharacterized protein PA4534
E: Uncharacterized protein PA4534
F: Uncharacterized protein PA4534
G: Uncharacterized protein PA4534
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,95921
Polymers108,8007
Non-polymers4,15914
Water11,764653
1
A: Uncharacterized protein PA4534
B: Uncharacterized protein PA4534
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,25710
Polymers31,0862
Non-polymers2,1728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-13 kcal/mol
Surface area12200 Å2
MethodPISA
2
C: Uncharacterized protein PA4534
D: Uncharacterized protein PA4534
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0795
Polymers31,0862
Non-polymers9943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-10 kcal/mol
Surface area12520 Å2
MethodPISA
3
E: Uncharacterized protein PA4534
F: Uncharacterized protein PA4534


Theoretical massNumber of molelcules
Total (without water)31,0862
Polymers31,0862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-11 kcal/mol
Surface area13000 Å2
MethodPISA
4
G: Uncharacterized protein PA4534
hetero molecules

G: Uncharacterized protein PA4534
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0738
Polymers31,0862
Non-polymers1,9886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area8700 Å2
ΔGint-14 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.116, 110.952, 294.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 137 / Label seq-ID: 1 - 137

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17BB
27CC
18BB
28DD
19BB
29EE
110BB
210FF
111BB
211GG
112CC
212DD
113CC
213EE
114CC
214FF
115CC
215GG
116DD
216EE
117DD
217FF
118DD
218GG
119EE
219FF
120EE
220GG
121FF
221GG

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

#1: Protein
Uncharacterized protein PA4534


Mass: 15542.815 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4534 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HVP3
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% polyethylene glycol (PEG) 3350, 0.2M Ammonium Citrate Dibasic, 0.1M Tris-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 308660 / % possible obs: 99.2 % / Redundancy: 18.3 % / Net I/σ(I): 52.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.021 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20676 7981 5 %RANDOM
Rwork0.19298 ---
obs0.19366 150961 99.22 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 46.064 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å2-0 Å2
2--0.1 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7665 0 264 653 8582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198210
X-RAY DIFFRACTIONr_bond_other_d0.0110.027885
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.98611129
X-RAY DIFFRACTIONr_angle_other_deg1.96317952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.91221.578412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.861151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.30915112
X-RAY DIFFRACTIONr_chiral_restr0.1020.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029230
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022110
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_it2.0461.5693863
X-RAY DIFFRACTIONr_mcbond_other2.0271.5673858
X-RAY DIFFRACTIONr_mcangle_it3.0512.3444819
X-RAY DIFFRACTIONr_mcangle_other3.0522.3444820
X-RAY DIFFRACTIONr_scbond_it3.0542.0124347
X-RAY DIFFRACTIONr_scbond_other3.0542.0124347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4652.8876296
X-RAY DIFFRACTIONr_long_range_B_refined8.14614.7279568
X-RAY DIFFRACTIONr_long_range_B_other8.14614.739569
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A161700.06
12B161700.06
21A160600.06
22C160600.06
31A156480.09
32D156480.09
41A157940.08
42E157940.08
51A152920.11
52F152920.11
61A161240.06
62G161240.06
71B160140.06
72C160140.06
81B154120.09
82D154120.09
91B156180.08
92E156180.08
101B152380.11
102F152380.11
111B160800.06
112G160800.06
121C155460.09
122D155460.09
131C158100.09
132E158100.09
141C152340.11
142F152340.11
151C160000.07
152G160000.07
161D153020.1
162E153020.1
171D147500.12
172F147500.12
181D153540.1
182G153540.1
191E151660.11
192F151660.11
201E155940.08
202G155940.08
211F151480.11
212G151480.11
LS refinement shellResolution: 1.653→1.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 564 -
Rwork0.222 10969 -
obs--98.59 %
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)
11.484-0.3944-0.28171.5957-0.05231.5079-0.1167-0.215-0.12030.2250.1153-0.21240.2060.11710.00150.11140.0542-0.02330.04770.01140.0572-19.158-16.107-41.105
21.38950.42370.12021.28140.10591.5973-0.09950.1569-0.111-0.20140.1315-0.22790.0420.1566-0.0320.0734-0.02950.04920.042-0.03690.0566-16.201-6.716-64.387
32.2678-1.297-0.68993.3357-1.06362.44260.10730.11940.53710.36060.0942-0.3284-0.5153-0.1975-0.20150.16440.07290.04960.04690.03410.1412-31.92918.718-44.056
42.3619-0.494-0.39581.9172-1.31263.0354-0.1655-0.60580.4250.95860.1504-0.5486-0.94750.44870.01510.66380.0177-0.22420.2935-0.16650.2306-22.99514.379-21.099
52.1132-0.96380.3662.1587-1.09925.641-0.0146-0.3418-0.16770.22180.54910.4724-0.1723-1.9058-0.53460.35840.21620.09730.89060.27590.1529-59.8310.389-22.369
61.6474-0.86081.99332.3914-1.56947.0578-0.2701-0.82250.10240.81440.60550.1682-1.5804-1.7893-0.33541.11660.59970.19550.85940.08780.1413-52.60718.9-0.046
71.45630.1673-0.11621.35170.20391.16260.0511-0.2019-0.14320.1745-0.04970.0326-0.0444-0.0372-0.00140.0475-0.01360.01010.03670.02580.0359-45.965-28.946-61.947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 137
2X-RAY DIFFRACTION2B1 - 137
3X-RAY DIFFRACTION3C1 - 137
4X-RAY DIFFRACTION4D1 - 137
5X-RAY DIFFRACTION5E1 - 137
6X-RAY DIFFRACTION6F1 - 137
7X-RAY DIFFRACTION7G1 - 137

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