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- PDB-7v5i: Structural insights into the substrate selectivity of acyl-CoA tr... -

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Basic information

Entry
Database: PDB / ID: 7v5i
TitleStructural insights into the substrate selectivity of acyl-CoA transferase
Components2-amino-3-ketobutyrate coenzyme A ligase
KeywordsTRANSFERASE / acyltransferase / pyridoxal phosphate / sphingolipids
Function / homology
Function and homology information


glycine C-acetyltransferase / glycine C-acetyltransferase activity / L-threonine catabolic process to glycine / ligase activity / pyridoxal phosphate binding / cytosol
Similarity search - Function
2-amino-3-ketobutyrate coenzyme A ligase / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...2-amino-3-ketobutyrate coenzyme A ligase / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 2-amino-3-ketobutyrate coenzyme A ligase
Similarity search - Component
Biological speciesVibrio proteolyticus NBRC 13287 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsChang, H.Y. / Ko, T.P.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2311-B-010-007-MY3 Taiwan
CitationJournal: Colloids Surf B Biointerfaces / Year: 2022
Title: Structural insights into the substrate selectivity of alpha-oxoamine synthases from marine Vibrio sp. QWI-06.
Authors: Chang, H.Y. / Lo, L.H. / Lan, Y.H. / Hong, M.X. / Chan, Y.T. / Ko, T.P. / Huang, Y.R. / Cheng, T.H. / Liaw, C.C.
History
DepositionAug 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
A: 2-amino-3-ketobutyrate coenzyme A ligase
B: 2-amino-3-ketobutyrate coenzyme A ligase
C: 2-amino-3-ketobutyrate coenzyme A ligase
D: 2-amino-3-ketobutyrate coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,9078
Polymers174,9194
Non-polymers9894
Water95553
1
A: 2-amino-3-ketobutyrate coenzyme A ligase
B: 2-amino-3-ketobutyrate coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9544
Polymers87,4592
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-49 kcal/mol
Surface area28320 Å2
MethodPISA
2
C: 2-amino-3-ketobutyrate coenzyme A ligase
D: 2-amino-3-ketobutyrate coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9544
Polymers87,4592
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-49 kcal/mol
Surface area29900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.121, 136.238, 219.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYSchain 'A'AA1 - 4001 - 400
12PLPPLPPLPPLPchain 'A'AE500
23ASNASNLYSLYSchain 'B'BB1 - 4001 - 400
24PLPPLPPLPPLPchain 'B'BF500
35ASNASNLYSLYSchain 'C'CC1 - 4001 - 400
36PLPPLPPLPPLPchain 'C'CG500
47ASNASNLYSLYSchain 'D'DD1 - 4001 - 400
48PLPPLPPLPPLPchain 'D'DH500

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Components

#1: Protein
2-amino-3-ketobutyrate coenzyme A ligase / AKB ligase / Glycine acetyltransferase


Mass: 43729.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio proteolyticus NBRC 13287 (bacteria)
Gene: kbl, VPR01S_15_00210 / Production host: Escherichia coli (E. coli) / References: UniProt: U3BPN5, glycine C-acetyltransferase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.0, with 23% polyethylene glycol (PEG) 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.07→30 Å / Num. obs: 36206 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 59.09 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.3
Reflection shellResolution: 3.07→3.18 Å / Rmerge(I) obs: 0.67 / Num. unique obs: 3586

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fc4

1fc4


Resolution: 3.08→27.41 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.759
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2488 1594 5 %
Rwork0.2043 30267 -
obs0.2065 31861 88.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.81 Å2
Refinement stepCycle: LAST / Resolution: 3.08→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12256 0 60 53 12369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002112504
X-RAY DIFFRACTIONf_angle_d0.481216860
X-RAY DIFFRACTIONf_chiral_restr0.04271888
X-RAY DIFFRACTIONf_plane_restr0.00412200
X-RAY DIFFRACTIONf_dihedral_angle_d10.56534580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.170.297730.26171381X-RAY DIFFRACTION44.89
3.17-3.290.28161010.22321932X-RAY DIFFRACTION63.51
3.29-3.420.27211230.22792348X-RAY DIFFRACTION76.48
3.42-3.570.26691450.22532724X-RAY DIFFRACTION88.88
3.57-3.760.27741590.21963023X-RAY DIFFRACTION98.18
3.76-40.21241610.19913075X-RAY DIFFRACTION99.81
4-4.30.261620.18683082X-RAY DIFFRACTION99.91
4.31-4.740.21871640.1733101X-RAY DIFFRACTION99.85
4.74-5.420.23151650.18413136X-RAY DIFFRACTION100
5.42-6.810.28331660.22883164X-RAY DIFFRACTION99.88
6.81-27.410.23591750.20553301X-RAY DIFFRACTION99.74
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)
11.98080.1366-0.14952.27650.01360.8927-0.11520.2581-0.2322-0.41550.2179-0.11670.0310.0021-0.05460.1805-0.0039-0.11990.23440.00210.271525.96454.96440.973
21.237-0.368-0.24331.67940.00680.874-0.3316-0.3977-0.39010.45040.23080.40210.1802-0.08230.03510.08970.1120.03860.35470.24030.343715.99355.30657.591
30.80151.0099-0.12571.48190.10520.35650.18250.4244-0.2786-0.54880.18530.68480.2484-0.12920.46020.3859-0.1358-0.39310.2458-0.17080.664818.2334.40741.627
42.2394-0.51360.05333.1723-0.01991.8566-0.03210.30620.1609-0.5161-0.02140.1644-0.2524-0.1390.03630.2082-0.034-0.06110.1880.05030.189327.59265.63140.253
51.85580.50980.58831.6154-0.21840.347-0.29410.04810.5460.02670.0993-0.9934-0.26930.0680.05960.0599-0.043-0.10230.2254-0.03090.839945.87665.61846.514
60.83780.66440.09372.0596-0.48720.2656-0.09320.48450.2711-0.73890.0782-0.3422-0.0667-0.11550.20270.5081-0.0408-0.08990.22440.40550.48233.54786.16335.586
70.75240.3576-0.03270.6826-0.25030.1075-0.2851-1.15530.04591.41320.11820.0949-0.25890.21990.12212.7240.1971-0.18782.87960.28080.981119.16459.667100.024
81.07460.41750.51311.0377-0.06842.5050.0682-0.8424-0.08651.5034-0.3969-0.993-0.1570.40470.28861.80580.3695-0.44712.25580.42331.034833.98256.27987.963
90.3446-0.24410.11980.4579-0.63931.27290.1471-0.8274-0.38190.972-0.0663-0.10430.4317-0.05020.18362.99540.06350.10142.50591.01191.286418.22137.72899.292
100.243-0.17280.06360.6158-0.13510.0333-0.0517-0.95520.30231.60960.01970.00240.0961-0.4171-0.05152.78790.38740.28532.9665-0.08421.12422.03869.748101.899
111.01420.40430.15250.1640.06480.02450.4084-0.88520.81890.9212-0.14030.5865-0.6961-0.0627-0.31052.72890.71190.63332.4478-0.19561.29648.38777.45690.169
120.00510.0013-0.01020-0.0040.01280.0341-0.2310.03890.7994-0.0409-0.0229-0.15190.57110.04313.8753-0.56690.20412.6788-0.26171.447223.7590.932107.882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )A1 - 129
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 280 )A130 - 280
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 400 )A281 - 400
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 129 )B1 - 129
5X-RAY DIFFRACTION5chain 'B' and (resid 130 through 280 )B130 - 280
6X-RAY DIFFRACTION6chain 'B' and (resid 281 through 400 )B281 - 400
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 129 )C1 - 129
8X-RAY DIFFRACTION8chain 'C' and (resid 130 through 280 )C130 - 280
9X-RAY DIFFRACTION9chain 'C' and (resid 281 through 400 )C281 - 400
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 129 )D1 - 129
11X-RAY DIFFRACTION11chain 'D' and (resid 130 through 280 )D130 - 280
12X-RAY DIFFRACTION12chain 'D' and (resid 281 through 400 )D281 - 400

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