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- PDB-7z79: Crystal structure of aminotransferase-like protein from Variovora... -

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Basic information

Entry
Database: PDB / ID: 7z79
TitleCrystal structure of aminotransferase-like protein from Variovorax paradoxus
ComponentsAminotransferase, class 4
KeywordsTRANSFERASE / Transaminase / BCAT / aminotransferase / catalytic lysine / catalytic asparagine / inactive
Function / homology
Function and homology information


transaminase activity
Similarity search - Function
Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Aminotransferase, class 4
Similarity search - Component
Biological speciesVariovorax paradoxus B4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBoyko, K.M. / Matyuta, I.O. / Nikolaeva, A.Y. / Khrenova, M.G. / Rakitina, T.V. / Popov, V.O. / Bezsudnova, E.Y.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Crystals / Year: 2022
Title: A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine
Authors: Boyko, K.M. / Matyuta, I.O. / Nikolaeva, A.Y. / Rakitina, T.V. / Popov, V.O. / Bezsudnova, E.Y. / Khrenova, M.G.
History
DepositionMar 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: Aminotransferase, class 4
B: Aminotransferase, class 4
C: Aminotransferase, class 4
D: Aminotransferase, class 4
E: Aminotransferase, class 4
F: Aminotransferase, class 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,10133
Polymers203,5836
Non-polymers3,51827
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31360 Å2
ΔGint-141 kcal/mol
Surface area55120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.299, 164.299, 190.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRLEULEUAA15 - 31315 - 313
21TYRTYRLEULEUBB15 - 31315 - 313
12ASPASPLEULEUAA18 - 31318 - 313
22ASPASPLEULEUCC18 - 31318 - 313
13ASPASPPROPROAA18 - 31418 - 314
23ASPASPPROPRODD18 - 31418 - 314
14ASPASPLEULEUAA18 - 31318 - 313
24ASPASPLEULEUEE18 - 31318 - 313
15PROPROPROPROAA17 - 31417 - 314
25PROPROPROPROFF17 - 31417 - 314
16ASPASPLEULEUBB18 - 31318 - 313
26ASPASPLEULEUCC18 - 31318 - 313
17ASPASPLEULEUBB18 - 31318 - 313
27ASPASPLEULEUDD18 - 31318 - 313
18ASPASPLEULEUBB18 - 31318 - 313
28ASPASPLEULEUEE18 - 31318 - 313
19PROPROLEULEUBB17 - 31317 - 313
29PROPROLEULEUFF17 - 31317 - 313
110ASPASPPROPROCC18 - 31418 - 314
210ASPASPPROPRODD18 - 31418 - 314
111ASPASPLEULEUCC18 - 31318 - 313
211ASPASPLEULEUEE18 - 31318 - 313
112ASPASPPROPROCC18 - 31418 - 314
212ASPASPPROPROFF18 - 31418 - 314
113ASPASPPROPRODD18 - 31418 - 314
213ASPASPPROPROEE18 - 31418 - 314
114ASPASPPROPRODD18 - 31418 - 314
214ASPASPPROPROFF18 - 31418 - 314
115ASPASPLEULEUEE18 - 31318 - 313
215ASPASPLEULEUFF18 - 31318 - 313

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Aminotransferase, class 4


Mass: 33930.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus B4 (bacteria) / Gene: VAPA_1c54540 / Production host: Escherichia coli (E. coli) / References: UniProt: T1XIY1

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Non-polymers , 5 types, 637 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.64 Å3/Da / Density % sol: 66.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 0.1 M Citric acid bistris propane pH 4.1, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→190.42 Å / Num. obs: 131283 / % possible obs: 99.7 % / Redundancy: 20.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.328 / Rpim(I) all: 0.073 / Rrim(I) all: 0.336 / Net I/σ(I): 7.5 / Num. measured all: 2691741
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3421.33.01913729464310.6350.6593.0910.899.5
12.6-190.4217.20.067157749150.9980.0170.06938.6100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CM0

5cm0


Resolution: 2.3→142.29 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.1957 / WRfactor Rwork: 0.183 / FOM work R set: 0.7693 / SU B: 15.272 / SU ML: 0.176 / SU R Cruickshank DPI: 0.2233 / SU Rfree: 0.1813 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 6635 5.1 %RANDOM
Rwork0.2054 ---
obs0.2066 124626 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.3 Å2 / Biso mean: 42.883 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 2.3→142.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13495 0 172 611 14278
Biso mean--56.53 37.3 -
Num. residues----1793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01214040
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.63119061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.51451797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14520.141778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.369152144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.51615146
X-RAY DIFFRACTIONr_chiral_restr0.150.21826
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210710
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A94400.07
12B94400.07
21A93040.07
22C93040.07
31A92200.07
32D92200.07
41A92180.08
42E92180.08
51A93190.07
52F93190.07
61B92680.08
62C92680.08
71B91920.07
72D91920.07
81B92150.08
82E92150.08
91B93030.06
92F93030.06
101C92400.07
102D92400.07
111C91850.08
112E91850.08
121C92990.07
122F92990.07
131D90930.07
132E90930.07
141D91890.06
142F91890.06
151E91630.08
152F91630.08
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 494 -
Rwork0.307 9116 -
all-9610 -
obs--99.31 %
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)
10.2129-0.0553-0.2810.1041-0.03880.5403-0.003-0.0403-0.0114-0.0022-0.02540.00820.00640.11670.02840.0739-0.0424-0.00310.08190.01140.012883.8331-56.414212.0123
20.45320.20850.0290.3185-0.13790.1355-0.01050.02210.0094-0.03080.01550.0323-0.03660.0209-0.0050.1156-0.0509-0.01780.02350.00620.011268.0771-39.5379-9.2782
30.03030.03270.09590.21250.2660.57360.032-0.03110.00450.043-0.03660.03090.063-0.05230.00450.0996-0.07080.020.0588-0.01870.013650.6309-62.74538.3857
40.0722-0.0013-0.13660.2272-0.2570.60480.02150.00660.00450.04310.00070.0387-0.1283-0.0344-0.02230.1249-0.01440.02640.022-0.02810.045548.2693-33.07628.4004
50.5650.34660.03040.28570.05150.0439-0.04570.0326-0.0368-0.03160.0374-0.03820.0353-0.01910.00830.1153-0.06720.00140.0442-0.01070.025250.4326-80.6814-0.5873
60.10030.12640.20080.38790.27320.5994-0.0418-0.01470.0607-0.0540.01790.0986-0.002-0.08470.0240.0618-0.0394-0.05760.05980.01270.09229.7548-57.1099-1.9016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 405
2X-RAY DIFFRACTION2B9 - 405
3X-RAY DIFFRACTION3C18 - 403
4X-RAY DIFFRACTION4D18 - 402
5X-RAY DIFFRACTION5E18 - 407
6X-RAY DIFFRACTION6F17 - 404

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