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- PDB-8rp7: Glutaminase subunit of aminodeoxychorismate synthase from Escheri... -

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Basic information

Entry
Database: PDB / ID: 8rp7
TitleGlutaminase subunit of aminodeoxychorismate synthase from Escherichia coli
ComponentsAminodeoxychorismate synthase component 2
KeywordsTRANSFERASE / glutamine amidotransferase folate biosynthesis
Function / homology
Function and homology information


aminodeoxychorismate synthase complex / aminodeoxychorismate synthase / 4-amino-4-deoxychorismate synthase activity / 4-aminobenzoate biosynthetic process / L-tryptophan biosynthetic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / protein heterodimerization activity
Similarity search - Function
Anthranilate synthase/para-aminobenzoate synthase like domain / : / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Aminodeoxychorismate synthase component 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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 2


Theoretical massNumber of molelcules
Total (without water)62,7333
Polymers62,7333
Non-polymers00
Water543
1
AAA: Aminodeoxychorismate synthase component 2


Theoretical massNumber of molelcules
Total (without water)20,9111
Polymers20,9111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Aminodeoxychorismate synthase component 2


Theoretical massNumber of molelcules
Total (without water)20,9111
Polymers20,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Aminodeoxychorismate synthase component 2


Theoretical massNumber of molelcules
Total (without water)20,9111
Polymers20,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.784, 115.582, 63.538
Angle α, β, γ (deg.)90.000, 101.062, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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.: 3
Source method: isolated from a genetically manipulated source
Details: 1. 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: sodium formate, PEG3350, L-glutamine

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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: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.82→42.423 Å / Num. obs: 12448 / % possible obs: 98.54 % / Redundancy: 5.1 % / CC1/2: 0.984 / Rmerge(I) obs: 0.3132 / Net I/σ(I): 6.84
Reflection shellResolution: 2.82→2.921 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.486 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 1221 / CC1/2: 0.513 / % possible all: 98.31

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→42.423 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.872 / SU B: 45.012 / SU ML: 0.394 / Cross valid method: FREE R-VALUE / ESU R Free: 0.473
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2679 638 5.132 %
Rwork0.2109 11793 -
all0.214 --
obs-12431 98.698 %
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: 51.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.186 Å2-0 Å21.105 Å2
2---1.185 Å2-0 Å2
3---0.527 Å2
Refinement stepCycle: LAST / Resolution: 2.82→42.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 0 3 4416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174188
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.6336166
X-RAY DIFFRACTIONr_angle_other_deg1.3871.5719692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7515566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.621.787235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.86415730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9491530
X-RAY DIFFRACTIONr_chiral_restr0.0760.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02960
X-RAY DIFFRACTIONr_nbd_refined0.2170.2852
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.24248
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22193
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22471
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1730.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2940.229
X-RAY DIFFRACTIONr_nbd_other0.3090.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.380.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_mcbond_it2.5824.2462270
X-RAY DIFFRACTIONr_mcbond_other2.5714.2442269
X-RAY DIFFRACTIONr_mcangle_it4.4746.3612834
X-RAY DIFFRACTIONr_mcangle_other4.4776.3632835
X-RAY DIFFRACTIONr_scbond_it2.5994.6482263
X-RAY DIFFRACTIONr_scbond_other2.5974.6492263
X-RAY DIFFRACTIONr_scangle_it4.4786.8193332
X-RAY DIFFRACTIONr_scangle_other4.4786.8193332
X-RAY DIFFRACTIONr_lrange_it11.9680.59718556
X-RAY DIFFRACTIONr_lrange_other11.9680.59618557
X-RAY DIFFRACTIONr_ncsr_local_group_10.150.055557
X-RAY DIFFRACTIONr_ncsr_local_group_20.170.055239
X-RAY DIFFRACTIONr_ncsr_local_group_30.180.055268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.8930.319380.297868X-RAY DIFFRACTION98.8004
2.893-2.9720.295430.265839X-RAY DIFFRACTION98.109
2.972-3.0580.263480.252846X-RAY DIFFRACTION98.8938
3.058-3.1520.282370.221781X-RAY DIFFRACTION98.5542
3.152-3.2550.307430.216745X-RAY DIFFRACTION97.8882
3.255-3.3690.32420.223785X-RAY DIFFRACTION98.8053
3.369-3.4960.243320.223704X-RAY DIFFRACTION98.2644
3.496-3.6380.287400.216692X-RAY DIFFRACTION98.1233
3.638-3.7990.256340.193680X-RAY DIFFRACTION99.0291
3.799-3.9840.221330.211648X-RAY DIFFRACTION98.5528
3.984-4.1990.254390.205605X-RAY DIFFRACTION99.0769
4.199-4.4520.262400.185563X-RAY DIFFRACTION98.5294
4.452-4.7580.193330.173536X-RAY DIFFRACTION100
4.758-5.1360.263290.174506X-RAY DIFFRACTION98.3456
5.136-5.6230.299260.203470X-RAY DIFFRACTION100
5.623-6.280.253230.236438X-RAY DIFFRACTION99.3534
6.28-7.240.281290.225373X-RAY DIFFRACTION99.0148
7.24-8.8370.348130.19318X-RAY DIFFRACTION99.3994
8.837-12.3740.1460.178258X-RAY DIFFRACTION98.8764
12.374-42.4230.555100.278138X-RAY DIFFRACTION95.4839
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.12390.0131-0.12852.16890.3242.0558-0.0523-0.0399-0.09650.02860.007-0.04980.07110.01850.04540.0055-0.00150.0110.06970.00170.0674-13.820914.691-18.0941
21.3194-0.32890.16183.39440.19081.81380.011-0.10110.05350.1469-0.0123-0.051-0.0615-0.04010.00120.01-0.0049-0.00070.1509-0.02350.0054-25.484935.14436.1946
30.9184-0.00590.23593.57330.091.6201-0.06230.08820.146-0.0876-0.017-0.1419-0.09020.04210.07930.0099-0.0038-0.00670.08510.06020.0571-37.620445.2409-23.5136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA-1 - 187
2X-RAY DIFFRACTION2ALLBBB-1 - 187
3X-RAY DIFFRACTION3ALLCCC-1 - 187

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