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- PDB-4cxr: Mycobaterium tuberculosis transaminase BioA complexed with 1-(1,3... -

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Basic information

Entry
Database: PDB / ID: 4cxr
TitleMycobaterium tuberculosis transaminase BioA complexed with 1-(1,3- benzothiazol-2-yl)methanamine
ComponentsADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
KeywordsTRANSFERASE / TRANSAMINASE / TUBERCULOSIS / PLP
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / 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 ...Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / 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
1-(1,3-benzothiazol-2-yl)methanamine / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDai, R. / Geders, T.W. / Finzel, B.C.
CitationJournal: Chembiochem / Year: 2014
Title: Inhibition of Mycobacterium Tuberculosis Transaminase Bioa by Aryl Hydrazines and Hydrazides.
Authors: Dai, R. / Wilson, D.J. / Geders, T.W. / Aldrich, C.C. / Finzel, B.C.
History
DepositionApr 8, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionApr 23, 2014ID: 4MQO
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
B: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9868
Polymers97,0732
Non-polymers9136
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-119.2 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.940, 66.084, 201.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE / 7 / 8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE / DAPA AT / DAPA AMINOTRANSFERASE / 7 / 8- ...7 / 8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE / DAPA AT / DAPA AMINOTRANSFERASE / 7 / 8-DIAMINONONANOATE SYNTHASE / DANS / DIAMINOPEL ARGONIC ACID SYNTHASE / MYCOBACTERIUM TUBERCULOSIS BIOA


Mass: 48536.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P0A4X6, UniProt: P9WQ81*PLUS, adenosylmethionine-8-amino-7-oxononanoate transaminase

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-2BG / 1-(1,3-benzothiazol-2-yl)methanamine


Mass: 164.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.16 Å3/Da / Density % sol: 43.13 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: VAPOR DIFFUSION, HANGING DROP PROTEIN: 25 MM HEPES, 50 MM NACL, 0.1 MM TCEP RESERVOIR:10% PEG 8000, 0.1M MAGNESIUM CHLORIDE, 0.1M HEPES CRYO: 15% PEG 400 IN RESERVOIR SOLUTION, VAPOR ...Details: VAPOR DIFFUSION, HANGING DROP PROTEIN: 25 MM HEPES, 50 MM NACL, 0.1 MM TCEP RESERVOIR:10% PEG 8000, 0.1M MAGNESIUM CHLORIDE, 0.1M HEPES CRYO: 15% PEG 400 IN RESERVOIR SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→97.48 Å / Num. obs: 86627 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 16.92 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.7→1.71 Å / Mean I/σ(I) obs: 3.8 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TFT

3tft


Resolution: 1.7→31.403 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 19.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2138 4557 5 %
Rwork0.1862 --
obs0.1876 86627 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→31.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6377 0 55 235 6667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066703
X-RAY DIFFRACTIONf_angle_d1.0679189
X-RAY DIFFRACTIONf_dihedral_angle_d12.8372348
X-RAY DIFFRACTIONf_chiral_restr0.041048
X-RAY DIFFRACTIONf_plane_restr0.0051181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.32331480.27772799X-RAY DIFFRACTION97
1.7193-1.73950.33811510.272848X-RAY DIFFRACTION97
1.7395-1.76080.27781360.25922831X-RAY DIFFRACTION97
1.7608-1.7830.27411510.24392807X-RAY DIFFRACTION96
1.783-1.80650.25951390.21872833X-RAY DIFFRACTION97
1.8065-1.83120.26621440.21172833X-RAY DIFFRACTION96
1.8312-1.85740.25561430.20972864X-RAY DIFFRACTION97
1.8574-1.88510.23911480.20172814X-RAY DIFFRACTION97
1.8851-1.91460.2781410.19762843X-RAY DIFFRACTION97
1.9146-1.9460.23691390.19962913X-RAY DIFFRACTION97
1.946-1.97950.2381650.19322818X-RAY DIFFRACTION98
1.9795-2.01550.22451470.19242855X-RAY DIFFRACTION97
2.0155-2.05430.2151400.18952900X-RAY DIFFRACTION99
2.0543-2.09620.22021690.19262779X-RAY DIFFRACTION95
2.0962-2.14180.23331660.19532867X-RAY DIFFRACTION99
2.1418-2.19160.22531400.19382902X-RAY DIFFRACTION98
2.1916-2.24640.21551610.18592870X-RAY DIFFRACTION97
2.2464-2.30710.20581480.18552900X-RAY DIFFRACTION99
2.3071-2.37490.21021480.18382904X-RAY DIFFRACTION98
2.3749-2.45160.23531630.19212906X-RAY DIFFRACTION98
2.4516-2.53920.2221650.19552919X-RAY DIFFRACTION98
2.5392-2.64080.23391550.19852883X-RAY DIFFRACTION98
2.6408-2.76090.24071700.19282923X-RAY DIFFRACTION98
2.7609-2.90630.22911570.19942898X-RAY DIFFRACTION98
2.9063-3.08830.20931590.19212879X-RAY DIFFRACTION97
3.0883-3.32650.22841390.19782983X-RAY DIFFRACTION98
3.3265-3.66080.19421470.17612962X-RAY DIFFRACTION98
3.6608-4.18950.17771570.15352971X-RAY DIFFRACTION98
4.1895-5.27420.14891660.14332958X-RAY DIFFRACTION97
5.2742-31.4080.17941550.16553151X-RAY DIFFRACTION98

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