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- PDB-3r4t: Crystal structure of 4-aminobutyrate aminotransferase GabT from M... -

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Basic information

Entry
Database: PDB / ID: 3r4t
TitleCrystal structure of 4-aminobutyrate aminotransferase GabT from Mycobacterium marinum covalently bound to pyridoxal phosphate
Components4-aminobutyrate aminotransferase GabT
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / tuberculosis / smegmatis / marinum / water contaminant / pyridoxal phosphate / PLP / LLP / gamma amino butyric acid / GABA / GABA transferase / Gabaculine / Phenelzine / Aminooxyacetic acid / Phenylethylidenehydrazine / Vigabatrin / Valproic acid
Function / homology
Function and homology information


(S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid metabolic process / L-arginine biosynthetic process / pyridoxal phosphate binding / identical protein 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) ...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-aminobutyrate aminotransferase
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Sep 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_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.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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-aminobutyrate aminotransferase GabT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0427
Polymers49,7591
Non-polymers2836
Water3,711206
1
A: 4-aminobutyrate aminotransferase GabT
hetero molecules

A: 4-aminobutyrate aminotransferase GabT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,08514
Polymers99,5192
Non-polymers56612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area11420 Å2
ΔGint-162 kcal/mol
Surface area26930 Å2
MethodPISA
2
A: 4-aminobutyrate aminotransferase GabT
hetero molecules

A: 4-aminobutyrate aminotransferase GabT
hetero molecules

A: 4-aminobutyrate aminotransferase GabT
hetero molecules

A: 4-aminobutyrate aminotransferase GabT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,17028
Polymers199,0384
Non-polymers1,13224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area27140 Å2
ΔGint-343 kcal/mol
Surface area49550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.620, 123.620, 157.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

21A-510-

HOH

31A-571-

HOH

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Components

#1: Protein 4-aminobutyrate aminotransferase GabT


Mass: 49759.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: gabT, MMAR_2118 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HN70
#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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MymaA.01026.b.A1 PW29968 at 27.8 mg/mL against JCSG+ screen condition D5, 70% MPD, 0.1 M Hepes pH 7.5, crystal tracking ID 220563d5, 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: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 26253 / Num. obs: 25245 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 37.813 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 15.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.5-2.579.10.5593.741676118341835100
2.57-2.640.4554.6164221793100
2.64-2.710.4025.23158401719100
2.71-2.80.3426.1315394167399.9
2.8-2.890.3096.85150681644100
2.89-2.990.2428.74144671586100
2.99-3.10.2119.86139711531100
3.1-3.230.17311.9134871478100
3.23-3.370.14714.04128371424100
3.37-3.540.11617.1122471363100
3.54-3.730.09719.68114821286100
3.73-3.950.08223.84109931248100
3.95-4.230.0726.67101831162100
4.23-4.560.06528.6695571102100
4.56-50.06129.28681100899.9
5-5.590.06726.687915927100
5.59-6.460.06325.757001828100
6.46-7.910.04631.386105715100
7.91-11.180.03239.494730574100
11.18-500.02738.41256734997.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.65 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.63 Å
Translation3 Å48.63 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3oks

3oks


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.1639 / WRfactor Rwork: 0.1327 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9004 / SU B: 11.939 / SU ML: 0.119 / SU R Cruickshank DPI: 0.2314 / SU Rfree: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1281 5.1 %RANDOM
Rwork0.1513 ---
obs0.1533 25110 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.63 Å2 / Biso mean: 28.8302 Å2 / Biso min: 6.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 13 206 3512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223352
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.984562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89923.913138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09515526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8411527
X-RAY DIFFRACTIONr_chiral_restr0.090.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212544
X-RAY DIFFRACTIONr_mcbond_it0.5411.52199
X-RAY DIFFRACTIONr_mcangle_it1.10723514
X-RAY DIFFRACTIONr_scbond_it2.26731153
X-RAY DIFFRACTIONr_scangle_it3.8744.51048
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 80 -
Rwork0.217 1744 -
all-1824 -
obs--99.4 %
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)
12.2418-0.9722-0.47661.11120.20361.22740.0072-0.12810.040.13260.0368-0.0927-0.03370.1429-0.0440.07850.0351-0.0360.1073-0.03560.05266.372760.879345.5608
20.19430.02340.18810.38470.00690.3342-0.0210.0144-0.0443-0.07640.0385-0.02550.00350.0446-0.01750.1080.04750.02850.0844-0.02690.053-6.134259.957822.3457
32.0763-0.16070.98871.29-0.74621.0043-0.02040.0899-0.2035-0.16560.0942-0.10980.0950.0383-0.07370.14520.04490.02440.0599-0.04530.0785-12.862537.831717.7486
40.6476-0.25190.30420.4399-0.21520.4844-0.0030.1105-0.0681-0.14120.0251-0.0544-0.00740.1151-0.02210.13050.02370.04040.1201-0.03590.0525-0.515455.508816.7927
51.49670.5355-0.26511.83260.25570.651-0.0362-0.1087-0.17040.06380.1066-0.13150.19040.0885-0.07050.13760.1011-0.01530.10240.0070.07276.129340.39936.093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 44
2X-RAY DIFFRACTION2A45 - 180
3X-RAY DIFFRACTION3A181 - 257
4X-RAY DIFFRACTION4A258 - 357
5X-RAY DIFFRACTION5A358 - 445

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