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- PDB-8onn: Crystal structure of D-amino acid aminotransferase from Aminobact... -

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Basic information

Entry
Database: PDB / ID: 8onn
TitleCrystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A complexed with 3-aminooxypropionic acid
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / Transaminase / point mutant / aminotransferase / complex / 3-aminooxypropionic acid
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transaminase activity
Similarity search - Function
: / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
Chem-OCF / Aminotransferase class IV
Similarity search - Component
Biological speciesAminobacterium colombiense (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Minyaev, M.E. / Shilova, S.A. / Bezsudnova, E.Y. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Biochem.J. / Year: 2023
Title: In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.
Authors: Shilova, S.A. / Matyuta, I.O. / Khrenova, M.G. / Nikolaeva, A.Y. / Klyachko, N.L. / Minyaev, M.E. / Khomutov, A.R. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionApr 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase class IV
B: Aminotransferase class IV
C: Aminotransferase class IV
D: Aminotransferase class IV
E: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,9319
Polymers154,5945
Non-polymers1,3374
Water2,864159
1
A: Aminotransferase class IV
B: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5064
Polymers61,8382
Non-polymers6682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area21830 Å2
2
C: Aminotransferase class IV
D: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5064
Polymers61,8382
Non-polymers6682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-28 kcal/mol
Surface area21590 Å2
3
E: Aminotransferase class IV

E: Aminotransferase class IV


Theoretical massNumber of molelcules
Total (without water)61,8382
Polymers61,8382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2250 Å2
ΔGint-18 kcal/mol
Surface area23750 Å2
Unit cell
Length a, b, c (Å)141.102, 51.335, 205.289
Angle α, β, γ (deg.)90.00, 110.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

21E-307-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Aminotransferase class IV


Mass: 30918.793 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aminobacterium colombiense (bacteria) / Gene: Amico_1844 / Production host: Escherichia coli (E. coli) / References: UniProt: D5EHC5
#2: Chemical
ChemComp-OCF / 3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid / PYRIDOXAMINE-5'-PHOSPHATE linked to 3-aminooxypropionic acid


Mass: 334.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.02M Sodium/potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.75268 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75268 Å / Relative weight: 1
ReflectionResolution: 2.1→47.55 Å / Num. obs: 79705 / % possible obs: 98 % / Redundancy: 4.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.063 / Rrim(I) all: 0.132 / Χ2: 0.92 / Net I/σ(I): 7.9 / Num. measured all: 333904
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 96.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.698 / Num. measured all: 18601 / Num. unique obs: 4502 / CC1/2: 0.658 / Rpim(I) all: 0.387 / Rrim(I) all: 0.8 / Χ2: 0.68 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACT4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.55 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.878 / SU B: 20.543 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29834 3973 5 %RANDOM
Rwork0.2559 ---
obs0.25809 75709 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.69 Å2
2--0.64 Å20 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10513 0 88 159 10760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01310868
X-RAY DIFFRACTIONr_bond_other_d0.0030.01510422
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.64814758
X-RAY DIFFRACTIONr_angle_other_deg1.3651.56524048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5251377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54521.429490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.154151851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1041573
X-RAY DIFFRACTIONr_chiral_restr0.10.21491
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212070
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022294
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_it1.9842.2665490
X-RAY DIFFRACTIONr_mcbond_other1.9842.2665489
X-RAY DIFFRACTIONr_mcangle_it3.1053.3926855
X-RAY DIFFRACTIONr_mcangle_other3.1053.3926856
X-RAY DIFFRACTIONr_scbond_it2.0662.3855378
X-RAY DIFFRACTIONr_scbond_other2.0672.3845375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2163.5097896
X-RAY DIFFRACTIONr_long_range_B_refined5.0626.31711406
X-RAY DIFFRACTIONr_long_range_B_other5.05726.29811394
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)
11A80130.09
12B80130.09
21A83280.09
22C83280.09
31A82540.1
32D82540.1
41A76590.13
42E76590.13
51B80150.09
52C80150.09
61B79860.09
62D79860.09
71B74450.12
72E74450.12
81C82180.09
82D82180.09
91C76220.13
92E76220.13
101D76360.13
102E76360.13
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 259 -
Rwork0.313 5563 -
obs--97.03 %
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)
10.13080.27170.09680.69240.00960.4003-0.0205-0.0101-0.0098-0.01030.0508-0.04870.0018-0.0713-0.03030.13340.0911-0.05150.1503-0.01250.26478.4841-0.193319.9936
21.7097-0.84550.25750.4283-0.13730.2652-0.05670.0728-0.28050.0489-0.00050.1478-0.07260.07730.05720.05060.0461-0.03590.1706-0.04110.427741.3445-2.827119.1819
30.0555-0.06880.23490.289-0.25721.13710.01670.0067-0.0135-0.0159-0.00590.05360.02680.0721-0.01080.10810.14960.00660.29250.00270.148317.99319.410761.8728
40.73380.2630.02530.1365-0.01340.5269-0.0412-0.0582-0.0530.05470.06630.0087-0.1496-0.0698-0.02510.15270.17620.0260.23420.01650.1577-9.635635.580954.5857
50.7307-0.52870.11470.6527-0.49970.68350.17830.063-0.0126-0.1572-0.12430.04620.06840.0778-0.05390.25140.03760.00840.1407-0.02280.1363-21.552856.517285.4199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 301
2X-RAY DIFFRACTION2B1 - 301
3X-RAY DIFFRACTION3C1 - 301
4X-RAY DIFFRACTION4D-1 - 301
5X-RAY DIFFRACTION5E1 - 275

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