[English] 日本語
Yorodumi
- PDB-8hx7: Crystal structure of 4-amino-4-deoxychorismate synthase from Stre... -

+
Open data


ID or keywords:

Loading...

-
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 / 4-aminobenzoate biosynthetic process / folic acid-containing compound biosynthetic process / glutamine metabolic 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 155 molecules

#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.: 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


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


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more