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- PDB-4e3r: PLP-bound aminotransferase mutant crystal structure from Vibrio f... -

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Basic information

Entry
Database: PDB / ID: 4e3r
TitlePLP-bound aminotransferase mutant crystal structure from Vibrio fluvialis
ComponentsPyruvate transaminase
KeywordsTRANSFERASE / aminotransferase
Function / homology
Function and homology information


organonitrogen compound metabolic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
Pyruvate transaminase
Similarity search - Component
Biological speciesVibrio fluvialis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMidelfort, K.S. / Kumar, R. / Han, S. / Karmilowicz, M.J. / McConnell, K. / Gehlhaar, D.K. / Mistry, A. / Chang, J.S. / Anderson, M. / Vilalobos, A. ...Midelfort, K.S. / Kumar, R. / Han, S. / Karmilowicz, M.J. / McConnell, K. / Gehlhaar, D.K. / Mistry, A. / Chang, J.S. / Anderson, M. / Vilalobos, A. / Minshull, J. / Govindarajan, S. / Wong, J.W.
CitationJournal: Protein Eng.Des.Sel. / Year: 2013
Title: Redesigning and characterizing the substrate specificity and activity of Vibrio fluvialis aminotransferase for the synthesis of imagabalin.
Authors: Midelfort, K.S. / Kumar, R. / Han, S. / Karmilowicz, M.J. / McConnell, K. / Gehlhaar, D.K. / Mistry, A. / Chang, J.S. / Anderson, M. / Villalobos, A. / Minshull, J. / Govindarajan, S. / Wong, J.W.
History
DepositionMar 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / software / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Pyruvate transaminase
B: Pyruvate transaminase
C: Pyruvate transaminase
D: Pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,17311
Polymers209,7934
Non-polymers3807
Water26,9681497
1
A: Pyruvate transaminase
B: Pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1356
Polymers104,8972
Non-polymers2384
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-76 kcal/mol
Surface area29750 Å2
MethodPISA
2
C: Pyruvate transaminase
D: Pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0395
Polymers104,8972
Non-polymers1423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-76 kcal/mol
Surface area29740 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.980, 161.940, 179.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pyruvate transaminase / aminotransferase


Mass: 52448.324 Da / Num. of mol.: 4
Mutation: F19W, W57F, F85A, R88K, V153A, K163F, I259V, R415F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fluvialis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: F2XBU9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1497 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG8000, 0.2M Lithium Sulfate, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 143088 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.63 Å2
Reflection shellResolution: 1.9→2 Å / % possible all: 83.1

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Processing

Software
NameVersionClassification
autoPROCdata collection
PHASERphasing
BUSTER2.9.3refinement
autoPROCdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.88 Å / Cor.coef. Fo:Fc: 0.9611 / Cor.coef. Fo:Fc free: 0.9522 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 7175 5.01 %RANDOM
Rwork0.1568 ---
all0.1584 143087 --
obs0.1584 143087 98.72 %-
Displacement parametersBiso mean: 27.78 Å2
Baniso -1Baniso -2Baniso -3
1--2.1489 Å20 Å20 Å2
2--3.8233 Å20 Å2
3----1.6744 Å2
Refine analyzeLuzzati coordinate error obs: 0.187 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14102 0 19 1497 15618
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114494HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0119666HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4838SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes324HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2134HARMONIC5
X-RAY DIFFRACTIONt_it14494HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion17.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1826SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18503SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2245 469 5.11 %
Rwork0.1867 8703 -
all0.1887 9172 -
obs--98.72 %
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)
10.26780.0617-0.02960.77460.00910.4912-0.0099-0.0003-0.0332-0.09790.0054-0.01780.0959-0.01250.0045-0.11480.0014-0.0016-0.1242-0.0025-0.1477-1.2743-35.556569.278
20.1809-0.09690.05680.7262-0.060.5869-0.0135-0.01330.0894-0.0721-0.0025-0.067-0.11520.01460.016-0.063-0.00510.0003-0.0692-0.0069-0.05620.0467-5.017970.4446
30.2550.00110.0370.73360.01590.67140.01260.01560.0670.0465-0.0076-0.005-0.1021-0.0019-0.005-0.06220.00590.0225-0.0760.0302-0.0650.2796-2.905921.6176
40.29120.0307-0.06860.6423-0.10180.7188-0.01230.0321-0.0425-0.0155-0.0303-0.06670.18260.03510.0426-0.11150.02040.0193-0.16460.0183-0.16511.4953-33.433319.9694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|451 }A2 - 451
2X-RAY DIFFRACTION2{ B|2 - B|453 }B2 - 453
3X-RAY DIFFRACTION3{ C|2 - C|451 }C2 - 451
4X-RAY DIFFRACTION4{ D|2 - D|451 }D2 - 451

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