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- PDB-3wwi: Crystal structure of the G136F mutant of the first R-stereoselect... -

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Basic information

Entry
Database: PDB / ID: 3wwi
TitleCrystal structure of the G136F mutant of the first R-stereoselective -transaminase identified from Arthrobacter sp. KNK168 (FERM-BP-5228)
Components(R)-amine transaminase
KeywordsTRANSFERASE / transaminase / amine-pyruvate aminotransferase / PYRIDOXAL-5'-PHOSPHATE / Multi-domain protein (alpha and beta) / Fold class IV PLP-dependent enzyme
Function / homology
Function and homology information


aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / cytosol
Similarity search - Function
Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel ...Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / (R)-amine transaminase
Similarity search - Component
Biological speciesArthrobacter sp. KNK168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsGuan, L.J. / Ohtsuka, J. / Miyakawa, T. / Zhi, Y. / Ito, N. / Yasohara, Y. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2015
Title: A new target region for changing the substrate specificity of amine transaminases.
Authors: Guan, L.J. / Ohtsuka, J. / Okai, M. / Miyakawa, T. / Mase, T. / Zhi, Y. / Hou, F. / Ito, N. / Iwasaki, A. / Yasohara, Y. / Tanokura, M.
History
DepositionJun 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 22, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms ...pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _struct_ref_seq_dif.details / _struct_site.details ..._struct_ref_seq_dif.details / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (R)-amine transaminase
B: (R)-amine transaminase
C: (R)-amine transaminase
D: (R)-amine transaminase
E: (R)-amine transaminase
F: (R)-amine transaminase
G: (R)-amine transaminase
H: (R)-amine transaminase
I: (R)-amine transaminase
J: (R)-amine transaminase
K: (R)-amine transaminase
L: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,48124
Polymers438,51512
Non-polymers2,96612
Water33,4361856
1
A: (R)-amine transaminase
B: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5804
Polymers73,0862
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-13 kcal/mol
Surface area24230 Å2
MethodPISA
2
C: (R)-amine transaminase
D: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5804
Polymers73,0862
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-15 kcal/mol
Surface area24100 Å2
MethodPISA
3
E: (R)-amine transaminase
L: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5804
Polymers73,0862
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-15 kcal/mol
Surface area24420 Å2
MethodPISA
4
F: (R)-amine transaminase
K: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5804
Polymers73,0862
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-13 kcal/mol
Surface area24240 Å2
MethodPISA
5
G: (R)-amine transaminase
J: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5804
Polymers73,0862
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-16 kcal/mol
Surface area24160 Å2
MethodPISA
6
H: (R)-amine transaminase
I: (R)-amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5804
Polymers73,0862
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-12 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.960, 134.280, 196.040
Angle α, β, γ (deg.)90.00, 100.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
(R)-amine transaminase / R-stereoselective-transaminase


Mass: 36542.945 Da / Num. of mol.: 12 / Mutation: G136F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. KNK168 (bacteria) / Gene: TAS / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: F7J696, EC: 2.1.6.18
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1856 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.2M magnesium chloride, 0.1M HEPES-HCl, 16% PEG 3350, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. all: 193164 / Num. obs: 190871 / % possible obs: 98.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.27→2.4 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.346 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21791 9595 5 %RANDOM
Rwork0.17097 ---
obs0.1733 181256 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.991 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0.92 Å2
2--0.33 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.27→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30292 0 180 1856 32328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01931228
X-RAY DIFFRACTIONr_bond_other_d0.0010.0229120
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.96242688
X-RAY DIFFRACTIONr_angle_other_deg0.783366884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02953852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54223.5541452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.675154792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.42515240
X-RAY DIFFRACTIONr_chiral_restr0.0810.24776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02135484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027140
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_it1.2262.17215444
X-RAY DIFFRACTIONr_mcbond_other1.2262.17215443
X-RAY DIFFRACTIONr_mcangle_it1.9993.25319284
X-RAY DIFFRACTIONr_mcangle_other1.9993.25319285
X-RAY DIFFRACTIONr_scbond_it1.5552.38415784
X-RAY DIFFRACTIONr_scbond_other1.5552.38415785
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5363.51323405
X-RAY DIFFRACTIONr_long_range_B_refined6.39918.67236958
X-RAY DIFFRACTIONr_long_range_B_other6.34618.27636286
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.267→2.326 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 682 -
Rwork0.298 12407 -
obs--92.18 %
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)
10.62060.1051-0.37381.1305-0.23130.74920.0235-0.0343-0.0331-0.03850.0335-0.0853-0.0820.1182-0.0570.1614-0.02130.02750.1996-0.02810.204190.007120.019846.5037
20.68490.2245-0.26761.03910.31480.90090.06420.10070.0060.01060.00880.0749-0.1562-0.1192-0.0730.17210.03720.02280.18680.02560.211857.336520.273553.3525
30.6188-0.0838-0.17960.8128-0.06850.9459-0.03920.0855-0.0365-0.07590.0371-0.07560.19480.02170.00210.23190.01580.03380.1515-0.03530.19280.609-20.828533.8477
40.59170.1427-0.0980.80180.08521.3543-0.0068-0.0018-0.02850.0810.02820.00650.2243-0.0721-0.02150.232-0.01690.01880.12540.00490.199965.1399-21.055763.3572
50.76850.04070.28230.99190.60662.2158-0.00680.03050.1774-0.014-0.078-0.0205-0.42120.16070.08480.15970.00590.03960.2238-0.03870.1813110.349727.077412.6361
61.0009-0.1470.03040.8063-0.27051.15730.03990.06420.0777-0.0239-0.00480.0009-0.123-0.0718-0.0350.18360.00820.02570.09930.01730.2402118.689228.962886.4155
70.79950.2043-0.0550.59880.02332.22870.02320.0622-0.01210.03860.05520.01360.2491-0.2025-0.07840.12710.05840.07090.26120.01640.141494.1652-6.0669-10.0516
80.81520.2649-0.00330.56690.13631.0893-0.04390.0407-0.0190.06110.03980.01460.0608-0.01960.00410.18530.0180.06950.1103-0.01330.24176.416761.035185.4165
90.84360.3035-0.28820.92190.28921.1408-0.04970.1731-0.0157-0.1040.1282-0.0767-0.14060.1054-0.07850.1822-0.05660.0840.189-0.01490.196196.47372.773361.3645
100.6686-0.2472-0.01020.9399-0.12272.0646-0.0102-0.23880.03440.1150.07750.059-0.117-0.3402-0.06730.1244-0.03790.10940.3668-0.01570.1096114.5585.458-33.854
111.0652-0.45560.16371.4124-0.24080.9498-0.0147-0.11-0.1465-0.03930.08120.3751-0.075-0.3344-0.06640.04170.02220.03990.20060.05390.357789.768816.546197.4669
121.05040.210.30281.33150.26370.74410.07490.32490.122-0.0701-0.1804-0.2957-0.01490.53220.10550.0354-0.02280.08490.59830.07780.2667139.3314.5741.633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 330
2X-RAY DIFFRACTION2B9 - 330
3X-RAY DIFFRACTION3C9 - 330
4X-RAY DIFFRACTION4D9 - 330
5X-RAY DIFFRACTION5E9 - 330
6X-RAY DIFFRACTION6F9 - 330
7X-RAY DIFFRACTION7G9 - 330
8X-RAY DIFFRACTION8H9 - 330
9X-RAY DIFFRACTION9I9 - 330
10X-RAY DIFFRACTION10J9 - 330
11X-RAY DIFFRACTION11K9 - 330
12X-RAY DIFFRACTION12L9 - 330

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