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- PDB-8hx7: Crystal structure of 4-amino-4-deoxychorismate synthase from Stre... -

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Basic information

Entry
Database: PDB / ID: 8hx7
TitleCrystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae co-crystallized with L-glutamine
Components4-amino-4-deoxychorismate synthase
KeywordsTRANSFERASE / Synthase / Multi-domain / Chorismate
Function / homology
Function and homology information


aminodeoxychorismate synthase / 4-amino-4-deoxychorismate synthase activity / folic acid-containing compound biosynthetic process / glutamine metabolic process
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 class-I / 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 class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
SUCCINIC ACID / TRYPTOPHAN / aminodeoxychorismate synthase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNakamichi, Y. / Watanabe, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other government1091195 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural basis for the allosteric pathway of 4-amino-4-deoxychorismate synthase.
Authors: Nakamichi, Y. / Kobayashi, J. / Toyoda, K. / Suda, M. / Hiraga, K. / Inui, M. / Watanabe, M.
History
DepositionJan 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-amino-4-deoxychorismate synthase
B: 4-amino-4-deoxychorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,24210
Polymers153,4892
Non-polymers7538
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-45 kcal/mol
Surface area46680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.291, 170.915, 160.344
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-amino-4-deoxychorismate synthase / aminodeoxychorismate synthase


Mass: 76744.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: papA / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6L8Q5, aminodeoxychorismate synthase

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Non-polymers , 5 types, 155 molecules

#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 51% (v/v) Tacsimate, 0.1 M Bis-tris propane (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→49.31 Å / Num. obs: 98481 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 40.29 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 17.66
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 9639 / CC1/2: 0.616 / Rpim(I) all: 0.797 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
MOLREP11.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QDL

1qdl


Resolution: 1.95→47.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 13.801 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24028 4924 5 %RANDOM
Rwork0.20996 ---
obs0.21148 93557 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.309 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å2-0 Å2
2---1.27 Å20 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.95→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10102 0 50 147 10299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01310376
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179722
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.64914089
X-RAY DIFFRACTIONr_angle_other_deg1.1321.57622331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81151304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56319.834604
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.947151618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.82415119
X-RAY DIFFRACTIONr_chiral_restr0.0470.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022464
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6723.0235246
X-RAY DIFFRACTIONr_mcbond_other0.6723.0235245
X-RAY DIFFRACTIONr_mcangle_it1.1454.5316540
X-RAY DIFFRACTIONr_mcangle_other1.1454.5316541
X-RAY DIFFRACTIONr_scbond_it0.5983.15130
X-RAY DIFFRACTIONr_scbond_other0.5943.0995129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0184.627550
X-RAY DIFFRACTIONr_long_range_B_refined3.58935.01710778
X-RAY DIFFRACTIONr_long_range_B_other3.58134.91610755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.997 Å
RfactorNum. reflection% reflection
Rfree0.339 354 -
Rwork0.356 6737 -
obs--98.08 %
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)
13.45881.1690.29772.5893-0.1315.40670.1086-0.0173-0.67770.101-0.019-0.6131.09670.8398-0.08960.38860.2922-0.09180.5902-0.05890.291-24.4266-37.004536.6909
21.77230.59511.02643.9406-0.31066.79690.10630.4503-0.22620.47130.2275-0.3690.62651.6116-0.33370.12630.1719-0.08230.8527-0.15380.1109-7.5798-8.258161.3251
31.37380.43381.87712.15381.62244.7869-0.32140.1570.2332-0.1216-0.02310.4925-0.63610.34470.34450.0982-0.0881-0.04050.46860.02810.1496-25.15834.517652.1868
44.1379-1.4547-0.07532.70490.37745.97180.11810.45020.7169-0.3884-0.061-0.315-0.40850.6173-0.05710.0907-0.0426-0.00780.59270.04630.2681-32.4214-3.769821.2357
52.8725-0.77690.83443.872-0.80982.7860.15050.67740.2333-0.6215-0.0617-0.0667-0.10360.4259-0.08880.35490.1606-0.0540.6613-0.05140.1792-41.7832-31.0894-7.0269
61.17920.63210.33141.86150.46471.89030.20990.1281-0.18450.0808-0.03420.15160.45010.0765-0.17570.27130.1857-0.14170.4655-0.07570.1951-45.7827-44.150312.3028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 194
2X-RAY DIFFRACTION2A195 - 396
3X-RAY DIFFRACTION3A397 - 701
4X-RAY DIFFRACTION4B-1 - 193
5X-RAY DIFFRACTION5B194 - 384
6X-RAY DIFFRACTION6B385 - 701

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