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- PDB-8rp1: Aminodeoxychorismate synthase complex from Escherichia coli, with... -

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Basic information

Entry
Database: PDB / ID: 8rp1
TitleAminodeoxychorismate synthase complex from Escherichia coli, with glutamine added
Components(Aminodeoxychorismate synthase component ...) x 2
KeywordsTRANSFERASE / glutamine amidotransferase folate biosynthesis
Function / homology
Function and homology information


aminodeoxychorismate synthase complex / aminodeoxychorismate synthase / tryptophan binding / 4-amino-4-deoxychorismate synthase activity / 4-aminobenzoate biosynthetic process / L-tryptophan biosynthetic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / protein heterodimerization activity / magnesium ion binding
Similarity search - Function
Aminodeoxychorismate synthase, component I / Anthranilate synthase/para-aminobenzoate synthase like domain / : / 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 / Glutamine amidotransferase ...Aminodeoxychorismate synthase, component I / Anthranilate synthase/para-aminobenzoate synthase like domain / : / 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 / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
GLUTAMIC ACID / TRYPTOPHAN / Aminodeoxychorismate synthase component 2 / Aminodeoxychorismate synthase component 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSung, S. / Franziska, J.F. / Schlee, S. / Sterner, R. / Wilmanns, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission664726European Union
CitationJournal: Acs Catalysis / Year: 2025
Title: Activity Regulation of a Glutamine Amidotransferase Bienzyme Complex by Substrate-Induced Subunit Interface Expansion.
Authors: Funke, F.J. / Schlee, S. / Bento, I. / Bourenkov, G. / Sterner, R. / Wilmanns, M.
History
DepositionJan 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Aminodeoxychorismate synthase component 2
BBB: Aminodeoxychorismate synthase component 2
CCC: Aminodeoxychorismate synthase component 1
DDD: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,99246
Polymers144,3994
Non-polymers3,59342
Water11,259625
1
AAA: Aminodeoxychorismate synthase component 2
DDD: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,01023
Polymers72,2002
Non-polymers1,81021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Aminodeoxychorismate synthase component 2
CCC: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,98223
Polymers72,2002
Non-polymers1,78321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.403, 109.912, 174.278
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Aminodeoxychorismate synthase component ... , 2 types, 4 molecules AAABBBCCCDDD

#1: Protein Aminodeoxychorismate synthase component 2 / ADC synthase / ADCS / 4-amino-4-deoxychorismate synthase component 2 / Aminodeoxychorismate ...ADC synthase / ADCS / 4-amino-4-deoxychorismate synthase component 2 / Aminodeoxychorismate synthase / glutamine amidotransferase component


Mass: 20853.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 1. The 'Gly, residue 0' (before the Met) comes from the Gly5-tag (N-terminal).
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pabA, b3360, JW3323 / Production host: Escherichia coli (E. coli) / References: UniProt: P00903, aminodeoxychorismate synthase
#2: Protein Aminodeoxychorismate synthase component 1 / ADC synthase / ADCS / 4-amino-4-deoxychorismate synthase component 1


Mass: 51345.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 1. The 'Gln, residue -2', 'Gly, residue -1' and 'His, residue 0' (before the Met) come from the TEV cleavge (N-terminal).
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pabB, b1812, JW1801 / Production host: Escherichia coli (E. coli) / References: UniProt: P05041, aminodeoxychorismate synthase

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Non-polymers , 8 types, 667 molecules

#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES, magnesium sulfate heptahydrate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.86→46.929 Å / Num. obs: 128415 / % possible obs: 99.96 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09922 / Net I/σ(I): 16.67
Reflection shellResolution: 1.86→1.926 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 12660 / CC1/2: 0.853 / % possible all: 99.98

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→46.929 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.816 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2014 6391 4.977 %
Rwork0.1668 122016 -
all0.168 --
obs-128407 99.976 %
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: 34.304 Å2
Baniso -1Baniso -2Baniso -3
1--1.265 Å2-0 Å20 Å2
2--2.117 Å2-0 Å2
3----0.852 Å2
Refinement stepCycle: LAST / Resolution: 1.86→46.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10139 0 198 625 10962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01310556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179593
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.63714344
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5722252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04251287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06822.158584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.395151712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0981576
X-RAY DIFFRACTIONr_chiral_restr0.0810.21352
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022229
X-RAY DIFFRACTIONr_nbd_refined0.2090.21955
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.29145
X-RAY DIFFRACTIONr_nbtor_refined0.1650.25053
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2520
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.237
X-RAY DIFFRACTIONr_nbd_other0.2660.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.227
X-RAY DIFFRACTIONr_mcbond_it3.2033.3535163
X-RAY DIFFRACTIONr_mcbond_other3.2033.3535162
X-RAY DIFFRACTIONr_mcangle_it4.175.0086445
X-RAY DIFFRACTIONr_mcangle_other4.1695.0086446
X-RAY DIFFRACTIONr_scbond_it4.53.9375393
X-RAY DIFFRACTIONr_scbond_other4.4953.9335386
X-RAY DIFFRACTIONr_scangle_it6.415.7037899
X-RAY DIFFRACTIONr_scangle_other6.4085.6967888
X-RAY DIFFRACTIONr_lrange_it7.80440.19911515
X-RAY DIFFRACTIONr_lrange_other7.80140.00511411
X-RAY DIFFRACTIONr_ncsr_local_group_10.1250.055716
X-RAY DIFFRACTIONr_ncsr_local_group_20.0880.0515007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.9080.2664440.2388952X-RAY DIFFRACTION100
1.908-1.9610.2644630.2188667X-RAY DIFFRACTION100
1.961-2.0170.2354410.1968497X-RAY DIFFRACTION100
2.017-2.0790.2394360.198248X-RAY DIFFRACTION99.9885
2.079-2.1480.2013990.1747998X-RAY DIFFRACTION99.9762
2.148-2.2230.213970.1677738X-RAY DIFFRACTION100
2.223-2.3070.2053970.1627433X-RAY DIFFRACTION100
2.307-2.4010.2153900.1697188X-RAY DIFFRACTION99.9868
2.401-2.5080.2023500.1646932X-RAY DIFFRACTION99.9863
2.508-2.630.2063410.1696616X-RAY DIFFRACTION99.9856
2.63-2.7720.2293400.1816269X-RAY DIFFRACTION100
2.772-2.940.2193400.1785955X-RAY DIFFRACTION100
2.94-3.1430.2322820.1825640X-RAY DIFFRACTION100
3.143-3.3940.1962930.1685224X-RAY DIFFRACTION99.9819
3.394-3.7180.1772480.1444843X-RAY DIFFRACTION100
3.718-4.1560.1662400.1344411X-RAY DIFFRACTION99.9785
4.156-4.7970.1442150.1233899X-RAY DIFFRACTION99.9757
4.797-5.8710.1991810.1683328X-RAY DIFFRACTION99.943
5.871-8.2870.2321220.192642X-RAY DIFFRACTION100
8.287-46.9290.216730.2071536X-RAY DIFFRACTION98.7723

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