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- PDB-3tat: TYROSINE AMINOTRANSFERASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 3tat
TitleTYROSINE AMINOTRANSFERASE FROM E. COLI
ComponentsTYROSINE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / AROMATIC SUBSTRATES / PLP ENZYME
Function / homology
Function and homology information


beta-methylphenylalanine transaminase / L-tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate / aromatic-amino-acid transaminase activity / aromatic-amino-acid transaminase / aspartate biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-leucine biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity ...beta-methylphenylalanine transaminase / L-tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate / aromatic-amino-acid transaminase activity / aromatic-amino-acid transaminase / aspartate biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-leucine biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / cytosol
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
PYRIDOXAL-5'-PHOSPHATE / Aromatic-amino-acid aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKo, T.P. / Yang, W.Z. / Wu, S.P. / Tsai, H. / Yuan, H.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary crystallographic analysis of the Escherichia coli tyrosine aminotransferase.
Authors: Ko, T.P. / Wu, S.P. / Yang, W.Z. / Tsai, H. / Yuan, H.S.
History
DepositionAug 12, 1998Processing site: BNL
Revision 1.0Aug 12, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: TYROSINE AMINOTRANSFERASE
B: TYROSINE AMINOTRANSFERASE
C: TYROSINE AMINOTRANSFERASE
D: TYROSINE AMINOTRANSFERASE
E: TYROSINE AMINOTRANSFERASE
F: TYROSINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,96112
Polymers261,4786
Non-polymers1,4836
Water00
1
A: TYROSINE AMINOTRANSFERASE
B: TYROSINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6544
Polymers87,1592
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-43 kcal/mol
Surface area29780 Å2
MethodPISA
2
C: TYROSINE AMINOTRANSFERASE
D: TYROSINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6544
Polymers87,1592
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-42 kcal/mol
Surface area30070 Å2
MethodPISA
3
E: TYROSINE AMINOTRANSFERASE
F: TYROSINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6544
Polymers87,1592
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-41 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.578, 126.578, 156.243
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.477432, 0.878567, -0.013403), (0.878586, -0.477541, -0.006477), (-0.012091, -0.008683, -0.999889)-0.5164, 0.7542, -6.3105
2given(0.965691, -0.251886, -0.063202), (0.250719, 0.967714, -0.025896), (0.067684, 0.009162, 0.997665)63.649, 35.4951, -10.9594
3given(0.239807, 0.969677, 0.047099), (0.970805, -0.239792, -0.00604), (0.005437, 0.047172, -0.998872)63.626, 35.9022, -17.5611
4given(-0.239087, -0.970587, -0.028261), (0.970986, -0.238839, -0.011898), (0.004799, -0.030285, 0.99953)0.5247, 72.8762, -1.8801
5given(-0.96911, 0.241082, 0.052012), (0.24162, 0.970362, 0.004242), (-0.049448, 0.016678, -0.998637)0.4496, 72.5684, -8.6353

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Components

#1: Protein
TYROSINE AMINOTRANSFERASE / PHEAT / TYRAT / AROAT


Mass: 43579.652 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: CONTAINS A PYRIDOXAL 5'-PHOSPHATE (PLP) COVALENTLY BOUND TO LYS 258
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: N4830-1 / Plasmid: PTC3 / Production host: Escherichia coli (E. coli)
References: UniProt: P04693, aromatic-amino-acid transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 2.7 Å3/Da / Density % sol: 48 %
Description: THE CRYSTAL DIFFRACTED ANISOTROPICALLY TO 3.5 A ALONG C-AXIS BUT ONLY TO 5.5 A ALONG A-B PLANE
Crystal growpH: 6.8 / Details: pH 6.8
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
28 %(w/v)PEG80001drop
30.5 mMphenylmethylsulfonyl fluoride1drop
40.05 mM1,4-dithiothreitol1drop
50.05 mMPLP1drop
612.5 mMphosphate1drop
710 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 19, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 13117 / % possible obs: 88.5 % / Redundancy: 5 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 14
Reflection shellResolution: 3.5→3.8 Å / Redundancy: 1 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 5 / Rsym value: 0.118 / % possible all: 1.5
Reflection
*PLUS
Num. measured all: 65956

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7AAT

7aat


Resolution: 3.5→30 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: STRICT NCS CONSTRAINT
RfactorNum. reflection% reflectionSelection details
Rfree0.26 991 8 %RANDOM
Rwork0.213 ---
obs0.213 12071 88.5 %-
Displacement parametersBiso mean: 56.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.35 Å
Luzzati d res low-30 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18390 0 90 0 18480
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.22
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.1341
X-RAY DIFFRACTIONx_mcangle_it0.2711.5
X-RAY DIFFRACTIONx_scbond_it0.2011.5
X-RAY DIFFRACTIONx_scangle_it0.3622.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : _ / Rms dev position: _ / Weight Biso : _ / Weight position: _

Ens-IDDom-IDNCS model details
11STRICT
22
33
44
LS refinement shellResolution: 3.5→3.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.277 6 -
Rfree-0 -
obs--33.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.PLPTOPH19.PEP
X-RAY DIFFRACTION3TOPOL.PLP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.64
LS refinement shell
*PLUS
Rfactor Rfree: 0

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