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- PDB-7qu9: Structure of aminodeoxychorismate synthase component 1 (PabB) fro... -

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Basic information

Entry
Database: PDB / ID: 7qu9
TitleStructure of aminodeoxychorismate synthase component 1 (PabB) from Bacillus subtilis spizizenii.
ComponentsAnthranilate synthase component I family protein
KeywordsTRANSFERASE / Chorismate / Magnesium / Folate
Function / homology
Function and homology information


Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHAN / Anthranilate synthase component I family protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsRooms, L.D. / Race, P.R. / Back, C.B. / Burton, N.B. / Willis, C.L. / Stach, J.E.M. / Duke, P.W. / Hawkins, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Defence Science and Technology Laboratory (DSTL) United Kingdom
CitationJournal: To Be Published
Title: Structure of aminodeoxychorismate synthase component 1 (PabB) from Bacillus subtilis spizizenii.
Authors: Rooms, L.D. / Race, P.R. / Back, C.B. / Burton, N.B. / Willis, C.L. / Stach, J.E.M. / Duke, P.W. / Hawkins, C.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anthranilate synthase component I family protein
B: Anthranilate synthase component I family protein
C: Anthranilate synthase component I family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,6408
Polymers159,8433
Non-polymers7975
Water6,251347
1
A: Anthranilate synthase component I family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6694
Polymers53,2811
Non-polymers3883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anthranilate synthase component I family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4852
Polymers53,2811
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Anthranilate synthase component I family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4852
Polymers53,2811
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.203, 91.466, 147.055
Angle α, β, γ (deg.)90.000, 90.950, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A23 - 501
2010B23 - 483
1020A23 - 501
2020C23 - 483
1030B23 - 484
2030C23 - 501

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Anthranilate synthase component I family protein


Mass: 53281.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: FAL52_19525 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5F2KFW0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.04 M potassium phosphate monobasic, 16 % (w/v) PEG8000, 20 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.14→91.49 Å / Num. obs: 85192 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.049 / Rrim(I) all: 0.126 / Net I/σ(I): 7 / Num. measured all: 559025 / Scaling rejects: 1410
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.14-2.26.62.0534107462200.620.8662.2321100
9.57-91.496.30.074635410140.9950.0320.08118.899.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CWA

5cwa


Resolution: 2.14→77.79 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2335 / WRfactor Rwork: 0.197 / FOM work R set: 0.7446 / SU B: 18.123 / SU ML: 0.209 / SU R Cruickshank DPI: 0.2343 / SU Rfree: 0.1827 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 4281 5 %RANDOM
Rwork0.1918 ---
obs0.1935 80872 99.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 154.48 Å2 / Biso mean: 64.548 Å2 / Biso min: 31.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å20.33 Å2
2--0.6 Å20 Å2
3----3.5 Å2
Refinement stepCycle: final / Resolution: 2.14→77.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10853 0 12 347 11212
Biso mean--104.57 64.23 -
Num. residues----1360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311153
X-RAY DIFFRACTIONr_bond_other_d0.0020.01710259
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.64315056
X-RAY DIFFRACTIONr_angle_other_deg1.2891.57723836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.97451349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96822.516620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.704151955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4381571
X-RAY DIFFRACTIONr_chiral_restr0.0740.21417
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022382
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A142220.1
12B142220.1
21A141090.12
22C141090.12
31B138800.12
32C138800.12
LS refinement shellResolution: 2.14→2.194 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.371 313 -
Rwork0.333 5825 -
obs--98.37 %
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)
11.8218-0.3699-0.20783.0540.59313.25410.02360.23950.0404-0.0408-0.0140.01290.3231-0.0213-0.00960.36750.06810.04610.08470.00120.10978.4189-16.963213.6268
21.9165-0.5143-0.18292.7443-0.04283.97380.0173-0.1320.2202-0.26930.0899-0.1282-0.27580.2668-0.10720.1932-0.08050.03980.1159-0.01790.12912.0598-18.518-37.2739
31.97130.40420.66443.1828-0.2163.96340.1686-0.19570.19630.497-0.2060.12180.3922-0.29240.03750.6891-0.06950.07090.0446-0.01860.156433.086827.2196-61.2171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 701
2X-RAY DIFFRACTION2B23 - 501
3X-RAY DIFFRACTION3C23 - 501

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