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- PDB-8rp2: Aminodeoxychorismate synthase complex from Escherichia coli, with... -

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Basic information

Entry
Database: PDB / ID: 8rp2
TitleAminodeoxychorismate synthase complex from Escherichia coli, with EDTA 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
TRYPTOPHAN / Aminodeoxychorismate synthase component 2 / Aminodeoxychorismate synthase component 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)145,93827
Polymers144,1434
Non-polymers1,79523
Water4,324240
1
AAA: Aminodeoxychorismate synthase component 2
hetero molecules

DDD: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,07715
Polymers72,0712
Non-polymers1,00613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2
BBB: Aminodeoxychorismate synthase component 2
CCC: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,86112
Polymers72,0712
Non-polymers78910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.965, 109.446, 178.859
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: The 'Gly, residue 0 and -1' (before the Met) come 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: 51160.465 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 , 7 types, 263 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.98→45.019 Å / Num. obs: 108431 / % possible obs: 99.94 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1027 / Net I/σ(I): 16.7
Reflection shellResolution: 1.98→2.051 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.034 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 10703 / CC1/2: 0.693 / % possible all: 99.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→45.019 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.278 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2388 5381 4.963 %
Rwork0.1999 103050 -
all0.202 --
obs-108431 99.978 %
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: 47.112 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å2-0 Å20 Å2
2--3.332 Å2-0 Å2
3----0.582 Å2
Refinement stepCycle: LAST / Resolution: 1.98→45.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10121 0 99 240 10460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310475
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179510
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.63814246
X-RAY DIFFRACTIONr_angle_other_deg1.2921.5722058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44351288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05822.192584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.954151704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3371575
X-RAY DIFFRACTIONr_chiral_restr0.0730.21351
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022229
X-RAY DIFFRACTIONr_nbd_refined0.1960.21877
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.28888
X-RAY DIFFRACTIONr_nbtor_refined0.1590.24971
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24875
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2920.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.224
X-RAY DIFFRACTIONr_nbd_other0.2060.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0770.27
X-RAY DIFFRACTIONr_mcbond_it3.8154.7325158
X-RAY DIFFRACTIONr_mcbond_other3.8154.7325157
X-RAY DIFFRACTIONr_mcangle_it5.2117.0816444
X-RAY DIFFRACTIONr_mcangle_other5.217.086445
X-RAY DIFFRACTIONr_scbond_it4.8335.3765317
X-RAY DIFFRACTIONr_scbond_other4.8215.3725314
X-RAY DIFFRACTIONr_scangle_it7.2587.8267802
X-RAY DIFFRACTIONr_scangle_other7.2527.827797
X-RAY DIFFRACTIONr_lrange_it9.0855.09911137
X-RAY DIFFRACTIONr_lrange_other9.08855.07411111
X-RAY DIFFRACTIONr_ncsr_local_group_10.1110.055631
X-RAY DIFFRACTIONr_ncsr_local_group_20.110.0514546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.0310.3474330.3257503X-RAY DIFFRACTION100
2.031-2.0870.3093740.2967327X-RAY DIFFRACTION99.987
2.087-2.1480.3243770.2757165X-RAY DIFFRACTION100
2.148-2.2140.2793940.2556905X-RAY DIFFRACTION100
2.214-2.2860.2643170.246777X-RAY DIFFRACTION100
2.286-2.3660.2793230.236546X-RAY DIFFRACTION99.9854
2.366-2.4560.2693040.2246327X-RAY DIFFRACTION100
2.456-2.5560.2833110.226097X-RAY DIFFRACTION100
2.556-2.6690.2623060.2165826X-RAY DIFFRACTION100
2.669-2.80.2612790.2145610X-RAY DIFFRACTION100
2.8-2.9510.2662980.2255287X-RAY DIFFRACTION99.9821
2.951-3.130.2772680.2195037X-RAY DIFFRACTION100
3.13-3.3450.2512770.2044693X-RAY DIFFRACTION100
3.345-3.6130.2052380.1794439X-RAY DIFFRACTION100
3.613-3.9570.2152110.1714116X-RAY DIFFRACTION100
3.957-4.4230.1952020.1623702X-RAY DIFFRACTION100
4.423-5.1060.1611480.1493328X-RAY DIFFRACTION100
5.106-6.2490.2611430.1882831X-RAY DIFFRACTION99.9328
6.249-8.8170.2021190.1672227X-RAY DIFFRACTION100
8.817-45.0190.23590.2121308X-RAY DIFFRACTION98.6292

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