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- PDB-3fsl: Crystal structure of tyrosine aminotransferase tripple mutant (P1... -

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Basic information

Entry
Database: PDB / ID: 3fsl
TitleCrystal structure of tyrosine aminotransferase tripple mutant (P181Q,R183G,A321K) from Escherichia coli at 2.35 A resolution
ComponentsAromatic-amino-acid aminotransferase
KeywordsTRANSFERASE / Tyrosine aminotransferase / pyridoxal phosphate / internal aldimine / Schiff base / Amino-acid biosynthesis / Aminotransferase / Aromatic amino acid biosynthesis
Function / homology
Function and homology information


beta-methylphenylalanine transaminase / L-tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate / aromatic-amino-acid:2-oxoglutarate aminotransferase activity / aromatic-amino-acid transaminase / L-phenylalanine:2-oxoglutarate aminotransferase activity / aspartate biosynthetic process / L-leucine:2-oxoglutarate aminotransferase activity / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / L-leucine biosynthetic process ...beta-methylphenylalanine transaminase / L-tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate / aromatic-amino-acid:2-oxoglutarate aminotransferase activity / aromatic-amino-acid transaminase / L-phenylalanine:2-oxoglutarate aminotransferase activity / aspartate biosynthetic process / L-leucine:2-oxoglutarate aminotransferase activity / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / L-leucine biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PLR / Aromatic-amino-acid aminotransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsMalashkevich, V.N. / Ng, B. / Kirsch, J.F.
CitationJournal: To be Published
Title: Crystal structure of tyrosine aminotransferase tripple mutant (P181Q,R183G,A321K) from Escherichia coli at 2.35 A resolution
Authors: Malashkevich, V.N. / Ng, B. / Kirsch, J.F.
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aromatic-amino-acid aminotransferase
B: Aromatic-amino-acid aminotransferase
C: Aromatic-amino-acid aminotransferase
D: Aromatic-amino-acid aminotransferase
E: Aromatic-amino-acid aminotransferase
F: Aromatic-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,81112
Polymers261,4126
Non-polymers1,3996
Water15,835879
1
A: Aromatic-amino-acid aminotransferase
B: Aromatic-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6044
Polymers87,1372
Non-polymers4662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-37 kcal/mol
Surface area29420 Å2
MethodPISA
2
C: Aromatic-amino-acid aminotransferase
D: Aromatic-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6044
Polymers87,1372
Non-polymers4662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-37 kcal/mol
Surface area29300 Å2
MethodPISA
3
E: Aromatic-amino-acid aminotransferase
F: Aromatic-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6044
Polymers87,1372
Non-polymers4662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-36 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.880, 119.160, 242.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -99999 - 99999 / Label seq-ID: -99999 - 99999

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsDIMER

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Components

#1: Protein
Aromatic-amino-acid aminotransferase / tyrosine aminotransferase / AROAT / ARAT


Mass: 43568.625 Da / Num. of mol.: 6 / Mutation: P171Q,R173G,A310K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: BL21List of strains of Escherichia coli / Gene: b4054, JW4014, tat, tyrB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P04693, aromatic-amino-acid transaminase
#2: Chemical
ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 879 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15-17% PEG4000, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.02 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 119658 / Redundancy: 2 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementResolution: 2.35→19.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.834 / SU B: 19.051 / SU ML: 0.201 / SU R Cruickshank DPI: 0.454 / SU Rfree: 0.278 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.454 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 5379 5 %RANDOM
Rwork0.213 ---
obs0.215 108457 90.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 97.44 Å2 / Biso mean: 34.885 Å2 / Biso min: 10.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18384 0 90 879 19353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02218828
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.96725512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71252346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28523.916858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.623153054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.57615132
X-RAY DIFFRACTIONr_chiral_restr0.1240.22826
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114352
X-RAY DIFFRACTIONr_mcbond_it1.131.511796
X-RAY DIFFRACTIONr_mcangle_it3.6382018780
X-RAY DIFFRACTIONr_scbond_it6.475207032
X-RAY DIFFRACTIONr_scangle_it4.3354.56732
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3079 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.160.05
BTIGHT POSITIONAL0.130.05
CTIGHT POSITIONAL0.150.05
DTIGHT POSITIONAL0.110.05
ETIGHT POSITIONAL0.120.05
FTIGHT POSITIONAL0.120.05
ATIGHT THERMAL0.20.5
BTIGHT THERMAL0.180.5
CTIGHT THERMAL0.190.5
DTIGHT THERMAL0.180.5
ETIGHT THERMAL0.180.5
FTIGHT THERMAL0.180.5
LS refinement shellResolution: 2.354→2.414 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 370 -
Rwork0.336 6653 -
all-7023 -
obs--81.3 %
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)
10.1770.2948-0.14410.494-0.2030.57370.00750.00920.0310.01430.00820.05230.0155-0.0958-0.01560.0013-0.00380.00180.0176-0.00030.005646.4438111.7166193.7323
20.73240.15810.14870.0816-0.14950.73140.0407-0.18610.0370.0234-0.04310.0075-0.0307-0.06190.00240.0261-0.03270.00030.0718-0.00730.002149.117599.7465227.172
30.36250.11050.02960.47450.12750.2006-0.00330.0107-0.09810.0371-0.01090.05740.1019-0.02290.01420.0543-0.01410.00720.017-0.00040.04580.815582.3864219.0536
40.6722-0.3781-0.01050.50280.00690.57370.01060.0459-0.2846-0.07470.00440.13040.1168-0.077-0.0150.0452-0.0265-0.00160.0205-0.02010.124116.396161.091195.016
50.73250.18680.01190.7435-0.13830.92480.07660.04720.0786-0.1227-0.06180.2654-0.1049-0.2634-0.01490.07170.0847-0.04620.1337-0.02790.11547.884881.0304141.0503
60.4019-0.18450.090.4749-0.09330.33610.01770.05720.1368-0.0785-0.0768-0.0652-0.05140.040.05910.0670.05370.010.07140.02870.061938.12398.3746149.6728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 409
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A1 - 1278
4X-RAY DIFFRACTION2B5 - 409
5X-RAY DIFFRACTION2B500
6X-RAY DIFFRACTION3C5 - 409
7X-RAY DIFFRACTION3C500
8X-RAY DIFFRACTION4D5 - 409
9X-RAY DIFFRACTION4D500
10X-RAY DIFFRACTION5E5 - 409
11X-RAY DIFFRACTION5E500
12X-RAY DIFFRACTION6F5 - 409
13X-RAY DIFFRACTION6F500

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