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- PDB-7pi1: Bacillus subtilis PabB -

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Basic information

Entry
Database: PDB / ID: 7pi1
TitleBacillus subtilis PabB
ComponentsAminodeoxychorismate synthase component 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


aminodeoxychorismate synthase / 4-amino-4-deoxychorismate synthase activity / folic acid biosynthetic process / tryptophan biosynthetic process / tetrahydrofolate biosynthetic process / magnesium ion binding
Similarity search - Function
Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme
Similarity search - Domain/homology
TRYPTOPHAN / Aminodeoxychorismate synthase component 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.729 Å
AuthorsRooms, L.D. / Race, P.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: To be published
Title: Crystal structure of Bacillus subtilis PabB, component 1.
Authors: Rooms, L.D. / Race, P.R. / Devine, A. / Willis, C.L. / Back, C.R. / Burton, N. / Sudol, A.
History
DepositionAug 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Aminodeoxychorismate synthase component 1
BBB: Aminodeoxychorismate synthase component 1
CCC: Aminodeoxychorismate synthase component 1
DDD: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,77212
Polymers221,8584
Non-polymers9148
Water20,2491124
1
AAA: Aminodeoxychorismate synthase component 1
hetero molecules


  • defined by author
  • Evidence: gel filtration, Monomeric after separation via size exclusion.
  • 55.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,4641
Non-polymers2292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Aminodeoxychorismate synthase component 1
hetero molecules


  • defined by author
  • 55.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,4641
Non-polymers2292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Aminodeoxychorismate synthase component 1
hetero molecules


  • defined by author
  • 55.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,4641
Non-polymers2292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Aminodeoxychorismate synthase component 1
hetero molecules


  • defined by author
  • 55.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,4641
Non-polymers2292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.084, 170.698, 224.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aminodeoxychorismate synthase component 1 / / ADC synthase / ADCS / 4-amino-4-deoxychorismate synthase component 1


Mass: 55464.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: pabB, pab, BSU00740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28820, aminodeoxychorismate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1124 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.06 M magnesium chloride hexahydrate, 0.06 M calcium chloride dihydrate, 20 % v/v PEG 500 MME, 10 % w/v PEG 20000, 0.01 M tris (base); BICINE, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.729→51.08 Å / Num. obs: 206370 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 22.91 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.094 / Net I/σ(I): 4.4
Reflection shellResolution: 1.729→1.76 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 10035 / CC1/2: 0.256

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model used not yet deposited

Resolution: 1.729→50.826 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.118
RfactorNum. reflection% reflection
Rfree0.236 10342 5.014 %
Rwork0.1989 195901 -
all0.201 --
obs-206243 99.891 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.044 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.054 Å2
Refinement stepCycle: LAST / Resolution: 1.729→50.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14629 0 64 1125 15818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01315075
X-RAY DIFFRACTIONr_bond_other_d0.0350.01713809
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.64420372
X-RAY DIFFRACTIONr_angle_other_deg2.3281.57632096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35651832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66422.704847
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.073152633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8311592
X-RAY DIFFRACTIONr_chiral_restr0.0670.21930
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216898
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023222
X-RAY DIFFRACTIONr_nbd_refined0.1940.22820
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.212348
X-RAY DIFFRACTIONr_nbtor_refined0.1650.26979
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.26799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.21020
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1140.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1790.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.240
X-RAY DIFFRACTIONr_nbd_other0.2430.2137
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.229
X-RAY DIFFRACTIONr_mcbond_it2.4763.5027331
X-RAY DIFFRACTIONr_mcbond_other2.4743.5017330
X-RAY DIFFRACTIONr_mcangle_it3.8065.2349138
X-RAY DIFFRACTIONr_mcangle_other3.8065.2359139
X-RAY DIFFRACTIONr_scbond_it3.393.9857744
X-RAY DIFFRACTIONr_scbond_other3.393.9837742
X-RAY DIFFRACTIONr_scangle_it5.5055.79111226
X-RAY DIFFRACTIONr_scangle_other5.5055.79111226
X-RAY DIFFRACTIONr_lrange_it7.63141.25516714
X-RAY DIFFRACTIONr_lrange_other7.57540.90916448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.729-1.7740.3887610.37414115X-RAY DIFFRACTION98.5818
1.774-1.8220.3767280.36814028X-RAY DIFFRACTION99.9932
1.822-1.8750.3626970.36113609X-RAY DIFFRACTION100
1.875-1.9330.3496890.34913154X-RAY DIFFRACTION100
1.933-1.9960.3356970.32612803X-RAY DIFFRACTION100
1.996-2.0660.3096680.29412426X-RAY DIFFRACTION100
2.066-2.1440.2916170.27412029X-RAY DIFFRACTION100
2.144-2.2310.2685990.25111573X-RAY DIFFRACTION100
2.231-2.330.2556100.22511078X-RAY DIFFRACTION100
2.33-2.4430.2435620.20510598X-RAY DIFFRACTION100
2.443-2.5750.2555370.19810113X-RAY DIFFRACTION100
2.575-2.7310.2484890.1889576X-RAY DIFFRACTION100
2.731-2.9190.2144950.1719026X-RAY DIFFRACTION100
2.919-3.1520.2194550.1678426X-RAY DIFFRACTION100
3.152-3.4520.2044050.1617804X-RAY DIFFRACTION100
3.452-3.8570.1973870.157064X-RAY DIFFRACTION100
3.857-4.4490.1752980.1336319X-RAY DIFFRACTION100
4.449-5.4390.182880.1385377X-RAY DIFFRACTION100
5.439-7.6480.2172290.1824250X-RAY DIFFRACTION100
7.648-50.8260.2131310.1772533X-RAY DIFFRACTION100

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