[English] 日本語
Yorodumi
- PDB-6sme: THE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM PROPIONIBACT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sme
TitleTHE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM PROPIONIBACTERIUM ACNES
Components3-dehydroquinate dehydratase
KeywordsBIOSYNTHETIC PROTEIN / SHIKIMATE PATHWAY DEHYDRATASE
Function / homology
Function and homology information


3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesCutibacterium acnes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsLapthorn, A.J. / Roszak, A.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/P00086X/1 United Kingdom
Citation
Journal: Nanoscale Horiz. / Year: 2020
Title: Biomacromolecular charge chirality detected using chiral plasmonic nanostructures
Authors: Rodier, M. / Keijzer, C. / Milner, J. / Karimullah, A. / Roszak, A.W. / Barron, L.D. / Gadegaard, N. / Lapthorn, A.J. / Kadodwala, M.
#1: Journal: Amb Express / Year: 2015
Title: Unraveling the kinetic diversity of microbial 3-dehydroquinate dehydratases of shikimate pathway.
Authors: Liu, C. / Liu, Y.M. / Sun, Q.L. / Jiang, C.Y. / Liu, S.J.
#2: Journal: Structure / Year: 2002
Title: The structure and mechanism of the type II dehydroquinase from Streptomyces coelicolor.
Authors: Roszak, A.W. / Robinson, D.A. / Krell, T. / Hunter, I.S. / Fredrickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionAug 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,16113
Polymers64,3094
Non-polymers8539
Water6,143341
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules

A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules

A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,48439
Polymers192,92612
Non-polymers2,55827
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area31550 Å2
ΔGint-297 kcal/mol
Surface area60800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.820, 128.820, 75.999
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

21A-390-

HOH

31B-383-

HOH

41D-271-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHRAA1 - 1424 - 145
21METMETTHRTHRBB1 - 1424 - 145
12METMETTHRTHRAA1 - 1424 - 145
22METMETTHRTHRCC1 - 1424 - 145
13SERSERASPASPAA2 - 1435 - 146
23SERSERASPASPDD2 - 1435 - 146
14HISHISTHRTHRBB0 - 1423 - 145
24HISHISTHRTHRCC0 - 1423 - 145
15SERSERASPASPBB2 - 1435 - 146
25SERSERASPASPDD2 - 1435 - 146
16SERSERASPASPCC2 - 1435 - 146
26SERSERASPASPDD2 - 1435 - 146

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
3-dehydroquinate dehydratase / 3-dehydroquinase / Type II DHQase


Mass: 16077.151 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutibacterium acnes (bacteria) / Gene: aroQ, CHT92_10435, CP876_09935 / Plasmid: PET28A+ / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A371N5G0, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.62 % / Description: rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 M Ammonium sulphate, 0.2 M sodium chloride, 0.1M TRIS pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.71
11-K, -H, -L20.29
ReflectionResolution: 1.66→64.41 Å / Num. obs: 71997 / % possible obs: 95.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 31.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1 / Redundancy: 7.3 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.71-1.771.341.536020.5110.5271.44264.6
4.859-64.410.05630.435970.9980.0220.0699.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.14 Å111.56 Å
Translation5.14 Å111.56 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSNov 11, 2017data reduction
Aimless0.6.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N7A

3n7a


Resolution: 1.7→64.41 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.106 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 3629 5.1 %RANDOM
Rwork0.1513 ---
obs0.1524 68108 89.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 153.09 Å2 / Biso mean: 28.437 Å2 / Biso min: 18.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.69 Å20 Å2
3----1.37 Å2
Refinement stepCycle: final / Resolution: 1.7→64.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 0 48 341 4764
Biso mean--50.86 39.76 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134569
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174229
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.6316236
X-RAY DIFFRACTIONr_angle_other_deg1.4371.5729733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92220.941255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58415729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8911543
X-RAY DIFFRACTIONr_chiral_restr0.0830.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02977
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43410.09
12B43410.09
21A43800.09
22C43800.09
31A41870.09
32D41870.09
41B43770.08
42C43770.08
51B41740.07
52D41740.07
61C41730.06
62D41730.06
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 60 -
Rwork0.497 1424 -
all-1484 -
obs--25.36 %
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)
10.0922-0.1057-0.08080.1955-0.04510.6028-0.02210.01080.01170.0186-0.0138-0.015-0.03390.04490.03590.0211-0.0145-0.01260.01940.02630.0442-36.587-21.7027.314
20.2322-0.01550.03370.32360.02870.39040.00020.058-0.0060.0180.0108-0.00680.00490.0482-0.01090.00420.00730.00910.04170.01320.03-36.878-39.375-17.766
30.3482-0.22680.12780.35510.02760.24640.03560.04590.0578-0.0333-0.1147-0.03140.0020.0190.07910.02190.00760.00440.05980.03290.0547-52.015-12.516-17.809
40.33930.0139-0.03360.1834-0.05390.2105-0.0104-0.02030.0133-0.0072-0.0196-0.0045-0.00070.00210.030.0148-0.0063-0.0080.01380.0060.0418-48.509-28.99326.846
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 144
2X-RAY DIFFRACTION2B0 - 144
3X-RAY DIFFRACTION3C0 - 144
4X-RAY DIFFRACTION4D0 - 144

+
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