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- PDB-8rp0: Aminodeoxychorismate synthase complex from Escherichia coli, with... -

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Basic information

Entry
Database: PDB / ID: 8rp0
TitleAminodeoxychorismate synthase complex from Escherichia coli, with glutamine and chorismate 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 / Chem-ISJ / TRYPTOPHAN / Aminodeoxychorismate synthase component 2 / Aminodeoxychorismate synthase component 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsSung, S. / Funke, F.J. / 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)146,61930
Polymers144,2574
Non-polymers2,36226
Water17,997999
1
AAA: Aminodeoxychorismate synthase component 2
DDD: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,39015
Polymers72,1282
Non-polymers1,26213
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)73,22915
Polymers72,1282
Non-polymers1,10013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.184, 109.946, 175.619
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: 20910.953 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: 51217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 1. The 'His, residue 0' (before the Met) comes 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, 1025 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ISJ / (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid / Chorismic Acid


Mass: 226.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O6 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
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: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.64→46.639 Å / Num. obs: 189833 / % possible obs: 99.97 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1203 / Net I/σ(I): 11.21
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.797 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 18781 / CC1/2: 0.677 / % possible all: 99.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→46.639 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.044 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1992 9423 4.964 %
Rwork0.1696 180410 -
all0.171 --
obs-189833 99.983 %
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: 33.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.824 Å20 Å2-0 Å2
2--1.706 Å2-0 Å2
3----0.882 Å2
Refinement stepCycle: LAST / Resolution: 1.64→46.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10145 0 142 999 11286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01310537
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179573
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6414316
X-RAY DIFFRACTIONr_angle_other_deg1.4171.57122194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.451288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75822.04593
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg3.142102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.998151719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1431577
X-RAY DIFFRACTIONr_chiral_restr0.0830.21356
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022249
X-RAY DIFFRACTIONr_nbd_refined0.220.21889
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.28948
X-RAY DIFFRACTIONr_nbtor_refined0.1630.24991
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24936
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2703
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.130.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.226
X-RAY DIFFRACTIONr_nbd_other0.2090.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.231
X-RAY DIFFRACTIONr_mcbond_it2.9613.2965164
X-RAY DIFFRACTIONr_mcbond_other2.963.2965163
X-RAY DIFFRACTIONr_mcangle_it4.0144.9296448
X-RAY DIFFRACTIONr_mcangle_other4.0144.9296449
X-RAY DIFFRACTIONr_scbond_it4.1933.7675373
X-RAY DIFFRACTIONr_scbond_other4.1893.7655366
X-RAY DIFFRACTIONr_scangle_it6.0525.4777868
X-RAY DIFFRACTIONr_scangle_other6.0455.4737857
X-RAY DIFFRACTIONr_lrange_it7.60739.71911610
X-RAY DIFFRACTIONr_lrange_other7.56139.16311357
X-RAY DIFFRACTIONr_ncsr_local_group_10.1330.055565
X-RAY DIFFRACTIONr_ncsr_local_group_20.0960.0514822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6830.3016430.28613246X-RAY DIFFRACTION100
1.683-1.7290.2716610.25212862X-RAY DIFFRACTION100
1.729-1.7790.2576730.23412536X-RAY DIFFRACTION100
1.779-1.8340.2686400.2212210X-RAY DIFFRACTION100
1.834-1.8940.2246200.211814X-RAY DIFFRACTION99.992
1.894-1.960.2265660.1911464X-RAY DIFFRACTION99.9668
1.96-2.0340.226000.18711052X-RAY DIFFRACTION99.9914
2.034-2.1170.2085290.17710676X-RAY DIFFRACTION100
2.117-2.2110.2075120.17410191X-RAY DIFFRACTION100
2.211-2.3190.2135160.1679789X-RAY DIFFRACTION100
2.319-2.4440.2015060.1639310X-RAY DIFFRACTION100
2.444-2.5920.1984930.1648795X-RAY DIFFRACTION100
2.592-2.7710.2164310.1698319X-RAY DIFFRACTION100
2.771-2.9930.2064080.1777740X-RAY DIFFRACTION100
2.993-3.2780.2113820.1857150X-RAY DIFFRACTION100
3.278-3.6650.2173450.1736516X-RAY DIFFRACTION99.9854
3.665-4.2310.1683320.1415738X-RAY DIFFRACTION100
4.231-5.1790.1392380.1194911X-RAY DIFFRACTION100
5.179-7.3130.1932050.1663873X-RAY DIFFRACTION100
7.313-46.6390.1791230.1862219X-RAY DIFFRACTION98.9856

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