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- PDB-6l1l: Apo-BacF structure from Bacillus subtillis -

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Basic information

Entry
Database: PDB / ID: 6l1l
TitleApo-BacF structure from Bacillus subtillis
ComponentsAminotransferase
KeywordsTRANSFERASE / Aminotransferase / PLP dependent enzyme
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / antibiotic biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aminotransferase / Transaminase BacF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBalasubramanian, G. / Deshmukh, A.A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India) India
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural insights into the catalytic mechanism of Bacillus subtilis BacF.
Authors: Deshmukh, A. / Gopal, B.
History
DepositionSep 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0004
Polymers89,5052
Non-polymers4942
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-34 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.220, 59.440, 84.230
Angle α, β, γ (deg.)90.000, 101.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminotransferase


Mass: 44752.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2089 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A164UM01, UniProt: P39643*PLUS, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.1M sodium acetate trihydrate, 0.1M sodium cacodylate trihydrate at pH 6.5, 30% w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→82.46 Å / Num. obs: 55815 / % possible obs: 99.43 % / Redundancy: 3 % / CC1/2: 0.985 / Net I/σ(I): 4.13
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 55815 / CC1/2: 0.985

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0103refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O1B

2o1b


Resolution: 1.9→82.46 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.975 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 2762 4.9 %RANDOM
Rwork0.2266 ---
obs0.2292 53052 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.92 Å2 / Biso mean: 30.559 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-1.96 Å2
2---0.92 Å20 Å2
3---2.36 Å2
Refinement stepCycle: final / Resolution: 1.9→82.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 30 268 6116
Biso mean--21.59 34.9 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196018
X-RAY DIFFRACTIONr_bond_other_d0.0060.025441
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9578207
X-RAY DIFFRACTIONr_angle_other_deg1.017312462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78723.946261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18315839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9541521
X-RAY DIFFRACTIONr_chiral_restr0.0810.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216964
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021433
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 204 -
Rwork0.315 3933 -
all-4137 -
obs--100 %

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