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- PDB-3q8n: Crystal structure of 4-aminobutyrate transaminase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3q8n
TitleCrystal structure of 4-aminobutyrate transaminase from Mycobacterium smegmatis
Components4-aminobutyrate transaminase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / 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
4-oxobutanoic acid / 4-aminobutyrate transaminase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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
DepositionJan 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 2023Group: 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_initial_refinement_model / 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 / _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: 4-aminobutyrate transaminase
B: 4-aminobutyrate transaminase
C: 4-aminobutyrate transaminase
D: 4-aminobutyrate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,1418
Polymers187,7334
Non-polymers4084
Water13,205733
1
A: 4-aminobutyrate transaminase
C: 4-aminobutyrate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0714
Polymers93,8662
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-43 kcal/mol
Surface area26890 Å2
MethodPISA
2
B: 4-aminobutyrate transaminase
D: 4-aminobutyrate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0714
Polymers93,8662
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-43 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.220, 98.410, 109.610
Angle α, β, γ (deg.)90.00, 111.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-aminobutyrate transaminase /


Mass: 46933.184 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_0581 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QQ04, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-SSN / 4-oxobutanoic acid / Succinic semialdehyde / Succinic semialdehyde


Mass: 102.089 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Internal tracking number 216475B10. PACT screen condition B10: 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG6000, MssmA.01026.b.A1 PW28765 at 25.2 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010
RadiationMonochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.05→19.76 Å / Num. all: 106925 / Num. obs: 100299 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.27 % / Biso Wilson estimate: 25.787 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.05-2.12.70.3493.3175757879650182.5
2.1-2.160.2643.819850687289.7
2.16-2.220.254.120381677790.8
2.22-2.290.225.515776557776.8
2.29-2.370.195.521125666895.1
2.37-2.450.1666.421252654396.2
2.45-2.540.157.221211636796.8
2.54-2.650.1388.120751614197.4
2.65-2.760.1259.219834589496.8
2.76-2.90.10610.319991571598.2
2.9-3.060.09411.419139543098.2
3.06-3.240.08113.418187512098.7
3.24-3.470.0715.516811486697.9
3.47-3.740.0651714941442296.7
3.74-4.10.05719.213788409496.9
4.1-4.580.04720.412847375498.6
4.58-5.290.04620.512003335299.2
5.29-6.480.04619.510593287799.4
6.48-9.170.03521.48125220599
9.170.02723.14014112488.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.81 Å
Translation2.5 Å19.81 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OKS

3oks


Resolution: 2.05→19.76 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.402 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 5025 5 %RANDOM
Rwork0.193 ---
all0.195 106925 --
obs0.195 100170 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.37 Å2
2---0.51 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12772 0 28 733 13533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213087
X-RAY DIFFRACTIONr_bond_other_d0.0010.028432
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.95917859
X-RAY DIFFRACTIONr_angle_other_deg0.952320624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25751766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95923.856529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.753151910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0451588
X-RAY DIFFRACTIONr_chiral_restr0.0830.22096
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022588
X-RAY DIFFRACTIONr_mcbond_it0.6471.58690
X-RAY DIFFRACTIONr_mcbond_other0.1791.53612
X-RAY DIFFRACTIONr_mcangle_it1.16213859
X-RAY DIFFRACTIONr_scbond_it2.15134397
X-RAY DIFFRACTIONr_scangle_it3.5044.53992
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 297 -
Rwork0.329 6109 -
all-6406 -
obs-6501 82.36 %
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)
10.29150.1134-0.06420.2301-0.04990.2602-0.0150.04070.0503-0.03240.01910.0288-0.0089-0.0471-0.0040.0124-0.004-0.00070.0150.00650.01761.37260.47-25.473
20.2957-0.0664-0.0190.26290.09690.3017-0.0529-0.045-0.05190.0610.03840.04090.0097-0.03280.01460.02140.01720.01820.01950.01420.018516.26561.00419.297
30.4060.06680.03740.2012-0.05160.3491-0.02030.0761-0.0169-0.04790.0164-0.03690.01270.05820.00390.0313-0.00550.0170.0227-0.0050.010330.90759.489-35.217
40.347-0.1073-0.06920.16120.04920.2234-0.0333-0.03330.01910.02680.0419-0.0346-0.00620.0652-0.00860.00670.003-0.00680.0242-0.00710.034345.74261.379.344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 450
2X-RAY DIFFRACTION2B1 - 450
3X-RAY DIFFRACTION3C1 - 450
4X-RAY DIFFRACTION4D1 - 450

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