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- PDB-4cxq: Mycobaterium tuberculosis transaminase BioA complexed with substr... -

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Basic information

Entry
Database: PDB / ID: 4cxq
TitleMycobaterium tuberculosis transaminase BioA complexed with substrate KAPA
ComponentsADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
KeywordsTRANSFERASE / TRANSAMINASE / TUBERCULOSIS
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
7-KETO-8-AMINOPELARGONIC ACID / DI(HYDROXYETHYL)ETHER / 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: 1.8 Å
AuthorsDai, R. / Wilson, D.J. / Geders, T.W. / Aldrich, C.C. / 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: 4MQN
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)98,34011
Polymers97,0732
Non-polymers1,2679
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13110 Å2
ΔGint-72.7 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.553, 66.149, 205.294
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, 535 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-KAP / 7-KETO-8-AMINOPELARGONIC ACID


Mass: 187.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.19 Å3/Da / Density % sol: 43.78 % / 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: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→98.9 Å / Num. obs: 79062 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4 / % possible all: 98.3

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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: 1.8→40.55 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 18.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 3956 5 %
Rwork0.1549 --
obs0.1569 79008 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6379 0 82 526 6987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076826
X-RAY DIFFRACTIONf_angle_d1.1049362
X-RAY DIFFRACTIONf_dihedral_angle_d13.3442433
X-RAY DIFFRACTIONf_chiral_restr0.0441078
X-RAY DIFFRACTIONf_plane_restr0.0051205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8220.25711280.18992644X-RAY DIFFRACTION98
1.822-1.8450.2461340.1892625X-RAY DIFFRACTION98
1.845-1.86930.22011360.17832609X-RAY DIFFRACTION98
1.8693-1.89490.22831410.17432678X-RAY DIFFRACTION98
1.8949-1.9220.20231360.17052574X-RAY DIFFRACTION98
1.922-1.95070.25251130.16652702X-RAY DIFFRACTION98
1.9507-1.98110.22561720.1692587X-RAY DIFFRACTION98
1.9811-2.01360.21831370.16582655X-RAY DIFFRACTION99
2.0136-2.04830.21351460.16522600X-RAY DIFFRACTION99
2.0483-2.08560.23861250.16872690X-RAY DIFFRACTION99
2.0856-2.12570.21931460.1682624X-RAY DIFFRACTION99
2.1257-2.16910.20381400.16442677X-RAY DIFFRACTION99
2.1691-2.21620.21881430.1592661X-RAY DIFFRACTION99
2.2162-2.26780.18821490.15722633X-RAY DIFFRACTION99
2.2678-2.32450.19391520.15282662X-RAY DIFFRACTION99
2.3245-2.38730.2081500.15792649X-RAY DIFFRACTION99
2.3873-2.45760.221270.15942683X-RAY DIFFRACTION99
2.4576-2.53690.20651420.16592688X-RAY DIFFRACTION99
2.5369-2.62750.2231380.16632687X-RAY DIFFRACTION99
2.6275-2.73270.20471560.16022672X-RAY DIFFRACTION99
2.7327-2.85710.19431520.16712674X-RAY DIFFRACTION99
2.8571-3.00770.18981380.16152720X-RAY DIFFRACTION99
3.0077-3.1960.20311420.16512686X-RAY DIFFRACTION100
3.196-3.44270.18631230.15892755X-RAY DIFFRACTION99
3.4427-3.78890.18831530.14862733X-RAY DIFFRACTION100
3.7889-4.33660.1591500.12472745X-RAY DIFFRACTION99
4.3366-5.46160.161370.12112802X-RAY DIFFRACTION100
5.4616-40.55990.1581500.15082937X-RAY DIFFRACTION99

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