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- PDB-8hx8: Crystal structure of 4-amino-4-deoxychorismate synthase from Stre... -

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Basic information

Entry
Database: PDB / ID: 8hx8
TitleCrystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae co-crystallized with chorismate
Components4-amino-4-deoxychorismate synthase
KeywordsTRANSFERASE / Synthase / Multi-domain / Chorismate
Function / homology
Function and homology information


aminodeoxychorismate synthase / 4-amino-4-deoxychorismate synthase activity / 4-aminobenzoate biosynthetic process / folic acid-containing compound biosynthetic process / L-tryptophan biosynthetic process / cytoplasm
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 / Glutamine amidotransferase class-I ...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
SUCCINIC ACID / TRYPTOPHAN / Aminodeoxychorismate synthase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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)154,0647
Polymers153,4892
Non-polymers5755
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-32 kcal/mol
Surface area46950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.334, 172.848, 161.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#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
#2: 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
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H6O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.86 %
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: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→47.51 Å / Num. obs: 45182 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 71.85 Å2 / CC1/2: 1 / Rpim(I) all: 0.033 / Net I/σ(I): 17.74
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 4425 / CC1/2: 0.58 / Rpim(I) all: 0.879 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
MOLREP11.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QDL

1qdl


Resolution: 2.55→47.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 46.041 / SU ML: 0.391 / Cross valid method: THROUGHOUT / ESU R: 1.33 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26799 2260 5 %RANDOM
Rwork0.20568 ---
obs0.20874 42924 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.698 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å20 Å2
2--8.41 Å20 Å2
3----8.83 Å2
Refinement stepCycle: 1 / Resolution: 2.55→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10275 0 40 2 10317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01210545
X-RAY DIFFRACTIONr_bond_other_d0.0020.0169529
X-RAY DIFFRACTIONr_angle_refined_deg0.841.65614325
X-RAY DIFFRACTIONr_angle_other_deg0.3011.5622160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78351328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.835123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.215101640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0390.21567
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022176
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_it2.0735.95336
X-RAY DIFFRACTIONr_mcbond_other2.0735.95336
X-RAY DIFFRACTIONr_mcangle_it3.3918.8466656
X-RAY DIFFRACTIONr_mcangle_other3.3918.8466657
X-RAY DIFFRACTIONr_scbond_it1.8446.0735209
X-RAY DIFFRACTIONr_scbond_other1.8446.0735210
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0619.0477670
X-RAY DIFFRACTIONr_long_range_B_refined5.00470.93211069
X-RAY DIFFRACTIONr_long_range_B_other5.00470.92911070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.612 Å
RfactorNum. reflection% reflection
Rfree0.493 164 -
Rwork0.4 3105 -
obs--98.91 %
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)
10.97410.61580.56381.54740.92332.4196-0.0902-0.0519-0.09270.00710.1441-0.04130.06730.6331-0.05380.08160.02260.0280.2280.04130.209629.1818-11.681150.7903
20.89860.35390.12152.51490.68291.5479-0.12830.3411-0.0345-0.59320.08960.05870.04250.19660.03870.31640.0521-0.02850.1804-0.01250.2998.9516-28.9649.738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 801
2X-RAY DIFFRACTION2B-1 - 701

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