[English] 日本語
Yorodumi
- PDB-4e8y: Crystal Structure of Burkholderia cenocepacia HldA in Complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e8y
TitleCrystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor
ComponentsD-beta-D-heptose 7-phosphate kinase
KeywordsTransferase/Transferase Inhibitor / LPS-heptose Biosynthesis / Beta-clasp Dimerization Region / PfkB Carbohydrate Kinase / Phosphorylation / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


phosphotransferase activity, alcohol group as acceptor / nucleotidyltransferase activity / kinase activity / carbohydrate metabolic process
Similarity search - Function
RfaE bifunctional protein, domain I / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IHA / : / Chem-M7B / PHOSPHATE ION / D-beta-D-heptose 7-phosphate kinase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, T.-W. / Verhey, T.B. / Junop, M.S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural-functional studies of Burkholderia cenocepacia D-glycero-beta-D-manno-heptose 7-phosphate kinase (HldA) and characterization of inhibitors with antibiotic adjuvant and antivirulence properties.
Authors: Lee, T.W. / Verhey, T.B. / Antiperovitch, P.A. / Atamanyuk, D. / Desroy, N. / Oliveira, C. / Denis, A. / Gerusz, V. / Drocourt, E. / Loutet, S.A. / Hamad, M.A. / Stanetty, C. / Andres, S.N. ...Authors: Lee, T.W. / Verhey, T.B. / Antiperovitch, P.A. / Atamanyuk, D. / Desroy, N. / Oliveira, C. / Denis, A. / Gerusz, V. / Drocourt, E. / Loutet, S.A. / Hamad, M.A. / Stanetty, C. / Andres, S.N. / Sugiman-Marangos, S. / Kosma, P. / Valvano, M.A. / Moreau, F. / Junop, M.S.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-beta-D-heptose 7-phosphate kinase
B: D-beta-D-heptose 7-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,18110
Polymers76,7392
Non-polymers1,4418
Water5,332296
1
A: D-beta-D-heptose 7-phosphate kinase
hetero molecules

A: D-beta-D-heptose 7-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,37610
Polymers76,7392
Non-polymers1,6368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3000 Å2
ΔGint-31 kcal/mol
Surface area25300 Å2
MethodPISA
2
B: D-beta-D-heptose 7-phosphate kinase
hetero molecules

B: D-beta-D-heptose 7-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,98510
Polymers76,7392
Non-polymers1,2468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3460 Å2
ΔGint-43 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.563, 69.200, 92.518
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-742-

HOH

21B-618-

HOH

31B-680-

HOH

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#1: Protein D-beta-D-heptose 7-phosphate kinase


Mass: 38369.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: hldA, BceJ2315_28810, BCAL2945 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EB35
#3: Sugar ChemComp-M7B / 7-O-phosphono-D-glycero-beta-D-manno-heptopyranose / 7-O-phosphono-D-glycero-beta-D-manno-heptose / 7-O-phosphono-D-glycero-D-manno-heptose / 7-O-phosphono-D-glycero-manno-heptose


Type: D-saccharide, beta linking / Mass: 290.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15O10P

-
Non-polymers , 5 types, 303 molecules

#2: Chemical ChemComp-IHA / {[2-({[5-(2,6-dimethoxyphenyl)-1,2,4-triazin-3-yl]amino}methyl)-1,3-benzothiazol-5-yl]oxy}acetic acid


Mass: 453.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N5O5S
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 20% PEG 10000, 8% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2010
RadiationMonochromator: Si 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.59→45.35 Å / Num. all: 20632 / Num. obs: 20632 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.59→2.64 Å / % possible all: 85.5

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E84

4e84


Resolution: 2.6→45.35 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1055 5.11 %RANDOM
Rwork0.1901 ---
obs0.1925 20626 --
all-20626 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.174 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8203 Å20 Å2-1.9478 Å2
2---4.586 Å2-0 Å2
3---2.7657 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 91 296 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014840
X-RAY DIFFRACTIONf_angle_d0.8566582
X-RAY DIFFRACTIONf_dihedral_angle_d18.3871801
X-RAY DIFFRACTIONf_chiral_restr0.047775
X-RAY DIFFRACTIONf_plane_restr0.004858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70560.32651390.25562345X-RAY DIFFRACTION83
2.7056-2.84820.25551200.22592513X-RAY DIFFRACTION88
2.8482-3.02660.30011280.22282527X-RAY DIFFRACTION88
3.0266-3.26030.28651400.21282461X-RAY DIFFRACTION87
3.2603-3.58820.25271210.18452481X-RAY DIFFRACTION87
3.5882-4.10720.18331330.16072446X-RAY DIFFRACTION85
4.1072-5.17340.20481490.14652417X-RAY DIFFRACTION85
5.1734-45.35990.22611250.20862381X-RAY DIFFRACTION81
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)
10.57250.3756-1.31141.5762-0.99992.71590.1146-0.1937-0.13460.0985-0.2678-0.4464-0.17340.47860.11660.22020.03-0.04660.36190.01240.35542.2194-0.156341.5155
21.36260.34-0.04452.3774-1.27881.09410.14120.1560.2383-0.0658-0.0250.0757-0.1228-0.0193-0.10490.26190.07740.01090.2404-0.02880.26050.38656.252128.5584
32.3842-0.1622-0.07772.66870.75652.08130.07250.1481-0.1656-0.2465-0.0898-0.14210.24360.13880.01230.36020.16320.01580.3799-0.01470.352713.5081-8.512922.6559
42.0007-1.64395.38442.00162.79762.00160.1199-0.25421.67320.336-0.6634-0.671-1.10120.14650.56340.80570.0314-0.03380.53130.0560.585221.23942.69937.7896
50.3323-0.26120.28372.3475-1.83673.67150.05170.0383-0.097-0.125-0.1151-0.13520.35550.14830.06020.19420.00660.01290.1848-0.04790.2437-5.30630.148558.0156
65.0508-1.24140.49323.3845-0.27083.55210.2009-0.4728-0.4260.3126-0.24160.09780.2307-0.19670.02590.2835-0.0721-0.01090.24130.01190.289-7.966229.403976.5941
74.01780.9574-1.33116.22440.30753.7662-0.0762-0.32461.03530.20290.01410.7092-0.7408-0.22690.08420.36280.0131-0.06480.2793-0.07750.4457-4.404245.706880.8536
82.39760.4204-0.4332.3711-0.19193.187-0.01560.20.0284-0.14650.0484-0.5350.02430.3471-0.03250.2712-0.0271-0.02760.31040.03040.320710.427938.135472.3814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:56 )A7 - 56
2X-RAY DIFFRACTION2( CHAIN A AND RESID 57:179 )A57 - 179
3X-RAY DIFFRACTION3( CHAIN A AND RESID 180:307 )A180 - 307
4X-RAY DIFFRACTION4( CHAIN A AND RESID 308:314 )A308 - 314
5X-RAY DIFFRACTION5( CHAIN B AND RESID 9:149 )B9 - 149
6X-RAY DIFFRACTION6( CHAIN B AND RESID 150:187 )B150 - 187
7X-RAY DIFFRACTION7( CHAIN B AND RESID 188:239 )B188 - 239
8X-RAY DIFFRACTION8( CHAIN B AND RESID 240:315 )B240 - 315

+
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