[English] 日本語
Yorodumi
- PDB-5f1u: biomimetic design results in a potent allosteric inhibitor of dih... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f1u
Titlebiomimetic design results in a potent allosteric inhibitor of dihydrodipicolinate synthase from Campylobacter jejuni
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE/LYASE inhibitor / schiff-base / aldolase / TIM barrel / LYASE-LYASE inhibitor complex
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-3VN / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsConly, C.J.T. / Palmer, D.R.J. / Sanders, D.A.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Biomimetic Design Results in a Potent Allosteric Inhibitor of Dihydrodipicolinate Synthase from Campylobacter jejuni.
Authors: Skovpen, Y.V. / Conly, C.J. / Sanders, D.A. / Palmer, D.R.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,89119
Polymers130,2544
Non-polymers1,63715
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-42 kcal/mol
Surface area39450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.590, 96.780, 145.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 32563.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: dapA / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

-
Non-polymers , 6 types, 317 molecules

#2: Chemical ChemComp-3VN / (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid / bis-Lysine


Mass: 318.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30N4O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsAuthors state that in ligand 3VN, carbonyl groups are de-protonated, and amine groups are protonated.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4000, 0.28 M NaAct, 0.1 mM TRIS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 1, 2013
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 47688 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.22 % / Biso Wilson estimate: 30.33 Å2 / Rmerge F obs: 0.991 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.324 / Χ2: 1.017 / Net I/σ(I): 11.71 / Num. measured all: 839254
Reflection shellResolution: 2.35→2.41 Å / Rmerge F obs: 0.005 / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 3.56 / Num. measured obs: 10632 / Num. possible: 26965 / Num. unique obs: 5464 / Rrim(I) all: 18.744 / Rejects: 0 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHENIX1.9_1692refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LER

3ler


Resolution: 2.35→48.39 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 2384 5 %
Rwork0.1706 45295 -
obs0.1735 47679 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.6 Å2 / Biso mean: 34.4077 Å2 / Biso min: 12.56 Å2
Refinement stepCycle: final / Resolution: 2.35→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9091 0 108 302 9501
Biso mean--45.81 35.33 -
Num. residues----1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039348
X-RAY DIFFRACTIONf_angle_d0.83412609
X-RAY DIFFRACTIONf_chiral_restr0.0321458
X-RAY DIFFRACTIONf_plane_restr0.0041607
X-RAY DIFFRACTIONf_dihedral_angle_d14.4563517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.35-2.39790.29611380.214926112749
2.3979-2.45010.27641380.213326182756
2.4501-2.50710.25521370.192826312768
2.5071-2.56980.24731390.199626382777
2.5698-2.63920.28061380.178726292767
2.6392-2.71690.2661390.187526412780
2.7169-2.80460.25721380.178826162754
2.8046-2.90480.25031390.186826462785
2.9048-3.02110.23951390.178726422781
3.0211-3.15860.22921400.175526542794
3.1586-3.32510.2831410.1826842825
3.3251-3.53330.24421390.181226402779
3.5333-3.8060.23351410.165926762817
3.806-4.18890.20031420.154126852827
4.1889-4.79450.18361410.143926862827
4.7945-6.03880.21941440.16327442888
6.0388-48.40020.18341510.153528543005
Refinement TLS params.Method: refined / Origin x: -6.451 Å / Origin y: 3.4065 Å / Origin z: 54.4349 Å
111213212223313233
T0.149 Å20.012 Å20.016 Å2-0.1338 Å20.0089 Å2--0.1388 Å2
L0.1405 °20.0538 °2-0.0281 °2-0.2904 °2-0.0217 °2--0.2606 °2
S-0.0017 Å °0.0064 Å °0.0261 Å °0.0915 Å °-0.0023 Å °0.0182 Å °-0.001 Å °-0.0052 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 298
2X-RAY DIFFRACTION1allB4 - 298
3X-RAY DIFFRACTION1allC3 - 298
4X-RAY DIFFRACTION1allD3 - 298
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1
10X-RAY DIFFRACTION1allJ1
11X-RAY DIFFRACTION1allK1
12X-RAY DIFFRACTION1allM1
13X-RAY DIFFRACTION1allO1
14X-RAY DIFFRACTION1allS1 - 347
15X-RAY DIFFRACTION1allN1
16X-RAY DIFFRACTION1allP1
17X-RAY DIFFRACTION1allQ1
18X-RAY DIFFRACTION1allT1
19X-RAY DIFFRACTION1allU1
20X-RAY DIFFRACTION1allV1

+
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