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- PDB-4f5i: Substrate Specificity Conversion of E. coli Pyridoxal-5'-Phosphat... -

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Basic information

Entry
Database: PDB / ID: 4f5i
TitleSubstrate Specificity Conversion of E. coli Pyridoxal-5'-Phosphate Dependent Aspartate Aminotransferase to Tyrosine Aminotransferase: Chimera P4.
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / Aminotransferase
Function / homology
Function and homology information


L-phenylalanine biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / aspartate catabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / 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
Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAddington, T.A. / Fisher, A.J. / Toney, M.D.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Janus: prediction and ranking of mutations required for functional interconversion of enzymes.
Authors: Addington, T.A. / Mertz, R.W. / Siegel, J.B. / Thompson, J.M. / Fisher, A.J. / Filkov, V. / Fleischman, N.M. / Suen, A.A. / Zhang, C. / Toney, M.D.
History
DepositionMay 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8293
Polymers89,7112
Non-polymers1181
Water13,385743
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-36 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.959, 103.065, 138.834
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 Aspartate aminotransferase / AspAT / Transaminase A


Mass: 44855.508 Da / Num. of mol.: 2
Mutation: I39V, N40D, L56M, N74T, T114S, S139T, S145A, V146I, F220I, F222I, A228G, Y254C, G259S, N295S, V385I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: AAT, aspC, b0928, JW0911 / Plasmid: pET45b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 14, 2010 / Details: Osmic Mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 44573 / Num. obs: 44527 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.14 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.0557 / Rsym value: 0.0557 / Net I/σ(I): 18.07
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 6.41 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.34 / Num. unique all: 4959 / Rsym value: 0.311 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.217 Å / SU ML: 0.62 / σ(F): 1.34 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 2149 4.84 %
Rwork0.1728 --
obs0.1747 44444 99.89 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.305 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7269 Å20 Å2-0 Å2
2--3.0667 Å2-0 Å2
3----3.7936 Å2
Refine analyzeLuzzati sigma a obs: 0.62 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6198 0 8 743 6949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086401
X-RAY DIFFRACTIONf_angle_d1.0398692
X-RAY DIFFRACTIONf_dihedral_angle_d12.9092340
X-RAY DIFFRACTIONf_chiral_restr0.07960
X-RAY DIFFRACTIONf_plane_restr0.0041146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25120.30161320.21632747X-RAY DIFFRACTION99
2.2512-2.30750.23881630.20652776X-RAY DIFFRACTION100
2.3075-2.36990.23271440.20862753X-RAY DIFFRACTION100
2.3699-2.43960.26921550.19452799X-RAY DIFFRACTION100
2.4396-2.51830.22211380.19532767X-RAY DIFFRACTION100
2.5183-2.60830.2181470.1852803X-RAY DIFFRACTION100
2.6083-2.71270.20831480.17982786X-RAY DIFFRACTION100
2.7127-2.83620.22391480.17842797X-RAY DIFFRACTION100
2.8362-2.98570.20311180.17712820X-RAY DIFFRACTION100
2.9857-3.17270.23561650.17512781X-RAY DIFFRACTION100
3.1727-3.41750.21631330.16992833X-RAY DIFFRACTION100
3.4175-3.76130.18531410.15792856X-RAY DIFFRACTION100
3.7613-4.30510.16021430.13962852X-RAY DIFFRACTION100
4.3051-5.42210.19141440.1432897X-RAY DIFFRACTION100
5.4221-42.22520.20821300.18523028X-RAY DIFFRACTION100
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)
10.266-0.2537-0.25130.2682-0.04161.41380.02520.13520.0277-0.0368-0.00320.0056-0.1308-0.18580.01850.1422-0.0041-0.02490.1920.02120.184824.613697.987940.101
22.2584-1.4514-0.28330.9706-0.08221.7787-0.0432-0.0327-0.39490.0636-0.02770.20770.42590.15480.04660.26850.01650.00150.14820.02920.222841.918674.946544.9383
30.55180.032-0.07790.5408-0.25991.92910.00850.0558-0.001-0.0935-0.0366-0.11440.08060.2780.00920.14520.02740.03270.15520.0090.162147.621490.027932.8471
40.85780.18250.03610.544-0.23411.123-0.03420.044-0.0418-0.0855-0.001-0.00940.2047-0.04740.00450.1577-0.01770.01050.1013-0.01170.135432.909584.621938.5186
51.5506-0.0293-0.00321.7178-0.52211.5448-0.08290.29890.351-0.2520.1590.00850.0696-0.2032-0.06490.2086-0.0264-0.02080.28080.0690.214828.020698.444315.1721
60.0482-0.13560.34670.3249-0.04531.6284-0.0470.0399-0.0324-0.00380.0038-0.02560.1090.06290.03220.1525-0.0151-0.00370.13550.01820.174231.752787.412659.4725
70.3025-0.2421-0.24572.145-0.26591.5929-0.05770.06380.1633-0.0580.08430.4643-0.3839-0.32450.08570.19970.0943-0.04080.26910.01760.204118.5452113.282654.3396
80.44760.0080.27320.45870.09741.6984-0.0564-0.07230.07340.053-0.0096-0.0666-0.25680.00230.0290.17680.0092-0.0360.1152-0.00580.168935.3418111.638266.1448
90.48810.0614-0.090.8586-0.41871.3508-0.01720.02440.0466-0.01080.0022-0.0108-0.1871-0.09570.02610.13780.0185-0.0130.13880.0020.131827.2863105.691352.4405
101.7722-0.74550.23771.0946-0.21881.3899-0.0241-0.23840.10860.09730.0204-0.10080.0236-0.07910.02610.1233-0.00710.00730.1676-0.00520.162228.466493.11981.3592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 7:81)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 82:104)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 105:253)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 254:341)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 342:406)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 7:81)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 82:104)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 105:244)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 245:310)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 311:406)

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