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- PDB-3oks: Crystal structure of 4-aminobutyrate transaminase from mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3oks
TitleCrystal structure of 4-aminobutyrate transaminase from mycobacterium smegmatis
Components4-aminobutyrate transaminase
KeywordsTRANSFERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
4-aminobutyrate aminotransferase, bacterial / 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 ...4-aminobutyrate aminotransferase, bacterial / 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
FORMIC ACID / 4-aminobutyrate transaminase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-aminobutyrate transaminase
B: 4-aminobutyrate transaminase
C: 4-aminobutyrate transaminase
D: 4-aminobutyrate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,54726
Polymers190,4124
Non-polymers1,13522
Water27,7611541
1
A: 4-aminobutyrate transaminase
B: 4-aminobutyrate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,77613
Polymers95,2062
Non-polymers57011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-43 kcal/mol
Surface area26110 Å2
MethodPISA
2
C: 4-aminobutyrate transaminase
D: 4-aminobutyrate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,77113
Polymers95,2062
Non-polymers56511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-44 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.010, 128.010, 104.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
4-aminobutyrate transaminase


Mass: 47602.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084/mc(2)155 / Gene: gabT, MSMEG_2959 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QWJ0, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1541 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: JCSG SCREEN CONDITION A5, TRAY BARCODE 216078: 200MM MG FORMATE PH 5.9, 20% PEG 3350, MYSMA.01026.C.A1 AT 25.11 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97741
20.97741
ReflectionResolution: 1.8→48.2 Å / Num. all: 155109 / Num. obs: 155089 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.35 % / Biso Wilson estimate: 19.82 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.91
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4 / Num. unique all: 11454 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Resolution: 1.8→48.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.813 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.159 7782 5 %RANDOM
Rwork0.126 ---
all0.128 155109 --
obs0.128 154935 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13110 0 73 1541 14724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213694
X-RAY DIFFRACTIONr_bond_other_d0.0010.029098
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.97418646
X-RAY DIFFRACTIONr_angle_other_deg0.957322257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79751867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97623.671553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.828152149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.99315103
X-RAY DIFFRACTIONr_chiral_restr0.0880.22149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022683
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_it0.7111.58959
X-RAY DIFFRACTIONr_mcbond_other0.2251.53726
X-RAY DIFFRACTIONr_mcangle_it1.235214325
X-RAY DIFFRACTIONr_scbond_it2.22634735
X-RAY DIFFRACTIONr_scangle_it3.6834.54277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 548 -
Rwork0.173 10886 -
obs--99.92 %
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)
10.3337-0.02440.11620.2229-0.08880.228-0.02980.00440.06380.0382-0.0197-0.0809-0.03380.04340.04950.0162-0.0078-0.02720.02370.00970.050313.58389.9326.004
20.33830.04940.11760.20760.01090.15110.0131-0.0568-0.04310.0313-0.0035-0.01080.0235-0.0307-0.00960.022-0.0049-0.01140.0310.01410.0153-10.85371.20911.094
30.253-0.0322-0.10150.14440.06340.2307-0.02360.0533-0.0493-0.0025-0.01990.03780.0441-0.05590.04350.0187-0.01340.01090.0287-0.0270.0318.10325.73816.952
40.2165-0.0076-0.15280.1255-0.01510.22970.0141-0.02510.01230.0047-0.0119-0.0052-0.01260.0373-0.00230.0117-0.00330.00720.0203-0.00820.009639.25346.04227.694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 445
2X-RAY DIFFRACTION2B0 - 445
3X-RAY DIFFRACTION3C0 - 445
4X-RAY DIFFRACTION4D0 - 445

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