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- PDB-8hx6: Crystal structure of 4-amino-4-deoxychorismate synthase from Stre... -

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Basic information

Entry
Database: PDB / ID: 8hx6
TitleCrystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae
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
D-MALATE / SUCCINIC ACID / TRYPTOPHAN / aminodeoxychorismate synthase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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)154,1747
Polymers153,4892
Non-polymers6855
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-23 kcal/mol
Surface area47240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.670, 171.405, 160.838
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, 56 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-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
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: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.14→47.27 Å / Num. obs: 74670 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 52.19 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 18.99
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.29 / Num. unique obs: 7224 / CC1/2: 0.64 / Rpim(I) all: 0.581 / % possible all: 98.1

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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: 2.14→47.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 25.22 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27161 3734 5 %RANDOM
Rwork0.22429 ---
obs0.22662 70936 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.996 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å2-0 Å20 Å2
2--5.66 Å20 Å2
3----4.04 Å2
Refinement stepCycle: 1 / Resolution: 2.14→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10107 0 48 51 10206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310398
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179722
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.6514124
X-RAY DIFFRACTIONr_angle_other_deg1.0611.57722342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31951306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8619.852609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.396151619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3615120
X-RAY DIFFRACTIONr_chiral_restr0.0380.21314
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211870
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022462
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_it0.8274.5295251
X-RAY DIFFRACTIONr_mcbond_other0.8274.5295250
X-RAY DIFFRACTIONr_mcangle_it1.5066.7886548
X-RAY DIFFRACTIONr_mcangle_other1.5066.7886549
X-RAY DIFFRACTIONr_scbond_it0.5784.6045147
X-RAY DIFFRACTIONr_scbond_other0.5784.6035146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.086.8767577
X-RAY DIFFRACTIONr_long_range_B_refined2.69351.19810547
X-RAY DIFFRACTIONr_long_range_B_other2.69251.19910547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.143→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 266 -
Rwork0.386 5059 -
obs--97.44 %
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)
10.84060.8257-0.81311.6041-1.13372.4518-0.02820.10990.09630.0970.150.0827-0.2073-0.558-0.12170.05130.0661-0.01650.15260.00360.0353-29.601610.8739-29.6756
20.90210.2555-0.38041.6382-0.95011.580.01410.281-0.0452-0.31060.0347-0.02-0.0231-0.2306-0.04870.19540.10240.02680.1516-0.01010.0858-8.36429.1068-71.1467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 801
2X-RAY DIFFRACTION2B-2 - 801

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