[English] 日本語
Yorodumi
- PDB-4kiw: Design and structural analysis of aromatic inhibitors of type II ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kiw
TitleDesign and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from Mycobacterium tuberculosis - compound 49e [5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid]
Components3-dehydroquinate dehydratase
KeywordsLyase/Lyase Inhibitor / dehydratase / Lyase-Lyase Inhibitor complex
Function / homology
Function and homology information


quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol
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
Chem-KIW / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsDias, M.V.B. / Howard, N.G. / Blundell, T.L. / Abell, C.
CitationJournal: Chemmedchem / Year: 2015
Title: Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase from Mycobacterium tuberculosis.
Authors: Howard, N.I. / Dias, M.V. / Peyrot, F. / Chen, L. / Schmidt, M.F. / Blundell, T.L. / Abell, C.
History
DepositionMay 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
G: 3-dehydroquinate dehydratase
H: 3-dehydroquinate dehydratase
I: 3-dehydroquinate dehydratase
J: 3-dehydroquinate dehydratase
K: 3-dehydroquinate dehydratase
L: 3-dehydroquinate dehydratase
M: 3-dehydroquinate dehydratase
N: 3-dehydroquinate dehydratase
O: 3-dehydroquinate dehydratase
P: 3-dehydroquinate dehydratase
Q: 3-dehydroquinate dehydratase
R: 3-dehydroquinate dehydratase
S: 3-dehydroquinate dehydratase
T: 3-dehydroquinate dehydratase
U: 3-dehydroquinate dehydratase
V: 3-dehydroquinate dehydratase
W: 3-dehydroquinate dehydratase
X: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,46146
Polymers431,50324
Non-polymers6,95822
Water19,8351101
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
G: 3-dehydroquinate dehydratase
H: 3-dehydroquinate dehydratase
I: 3-dehydroquinate dehydratase
J: 3-dehydroquinate dehydratase
K: 3-dehydroquinate dehydratase
L: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,91422
Polymers215,75212
Non-polymers3,16310
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26630 Å2
ΔGint-42 kcal/mol
Surface area55580 Å2
MethodPISA
2
M: 3-dehydroquinate dehydratase
N: 3-dehydroquinate dehydratase
O: 3-dehydroquinate dehydratase
P: 3-dehydroquinate dehydratase
Q: 3-dehydroquinate dehydratase
R: 3-dehydroquinate dehydratase
S: 3-dehydroquinate dehydratase
T: 3-dehydroquinate dehydratase
U: 3-dehydroquinate dehydratase
V: 3-dehydroquinate dehydratase
W: 3-dehydroquinate dehydratase
X: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,54724
Polymers215,75212
Non-polymers3,79512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26450 Å2
ΔGint-47 kcal/mol
Surface area55090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.710, 135.220, 143.910
Angle α, β, γ (deg.)90.00, 97.18, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 17979.303 Da / Num. of mol.: 24 / Fragment: aroD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroD, aroQ, MT2612, MTCY159.19, Rv2537c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical...
ChemComp-KIW / 5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid


Mass: 316.266 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C15H12N2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1101 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.8
Details: 0.15M KBr, 30% PEG 5000, pH 7.8, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9716 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2009
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 2.57→142.781 Å / Num. all: 99630 / Num. obs: 99630 / % possible obs: 85.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.139 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.57-2.714.10.74710.747185.3
2.71-2.874.10.5051.40.505185.6
2.87-3.074.10.3422.20.342186.5
3.07-3.324.10.2153.40.215187.1
3.32-3.634.10.1464.90.146187.1
3.63-4.064.10.1016.80.101186.4
4.06-4.694.20.0797.50.079185.5
4.69-5.754.10.1075.30.107184.8
5.75-8.134.10.0698.30.069182.8
8.13-67.614.40.03715.70.037181.6

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→67.61 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.856 / Occupancy max: 1 / Occupancy min: 0 / SU B: 15.433 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: LARGE DIFFERENCE BETWEEN R_FREE AND R_WORK, HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29379 4996 5 %RANDOM
Rwork0.19716 ---
obs0.20195 94578 85.21 %-
all-99630 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20.01 Å2
2--0 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.57→67.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25342 0 506 1101 26949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01926302
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.98335813
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40253318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19223.3851152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.537154107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.98215226
X-RAY DIFFRACTIONr_chiral_restr0.0970.24181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120108
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9053.6313368
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1055.43216654
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0833.81312934
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 376 -
Rwork0.331 6957 -
obs--84.95 %

+
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