[English] 日本語
Yorodumi
- PDB-9gn6: Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumonia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gn6
TitleCrystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae in complex with the inhibitor SAHA
ComponentsDeacetylase
KeywordsHYDROLASE / Inhibitor / SAHA / Deacetylase in Complex with SAHA
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrolase activity
Similarity search - Function
: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / Deacetylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. ozaenae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsQin, C. / Graf, L.G. / Schulze, S. / Palm, G.J. / Lammers, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA2984/6-1 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Distribution and diversity of classical deacylases in bacteria.
Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. ...Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. / Albrecht, D. / Zuhlke, D. / Sievers, S. / Strugnell, R.A. / Olsen, C.A. / Hofmann, K. / Lammers, M.
History
DepositionAug 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0255
Polymers41,6171
Non-polymers4084
Water4,179232
1
A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,10020
Polymers166,4694
Non-polymers1,63216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area17640 Å2
ΔGint-224 kcal/mol
Surface area42690 Å2
Unit cell
Length a, b, c (Å)146.206, 146.206, 146.206
Angle α, β, γ (deg.)90, 90, 90
Int Tables number197
Space group name H-MI23
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Deacetylase


Mass: 41617.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His6-tagged fusion-protein
Source: (gene. exp.) Klebsiella pneumoniae subsp. ozaenae (bacteria)
Strain: NCTC10313 / Gene: hdaH, NCTC10313_02007, NCTC5050_05964 / Plasmid: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A377Z5F6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2% (w/v) PEG 8000, 10% (v/v) glycerol and 0.5M KCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2019 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.3 Å / Num. obs: 37885 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 41.09 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.02 / Rrim(I) all: 0.028 / Net I/σ(I): 16.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2642 / CC1/2: 0.532 / Rpim(I) all: 0.597 / Rrim(I) all: 0.844 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSMar 15, 2019 BUILT=20190315data reduction
XDSMar 15, 2019 BUILT=20190315data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.277 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / SU B: 5.718 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1756 1859 4.909 %
Rwork0.1373 36012 -
all0.139 --
obs-37871 99.989 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.525 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 22 232 3076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122914
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162718
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.8143949
X-RAY DIFFRACTIONr_angle_other_deg0.6471.7466256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.305524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01710458
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.89110136
X-RAY DIFFRACTIONr_chiral_restr0.0930.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.2380.2639
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22552
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21454
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2540.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.210
X-RAY DIFFRACTIONr_nbd_other0.1450.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1070.222
X-RAY DIFFRACTIONr_mcbond_it3.3923.6081481
X-RAY DIFFRACTIONr_mcbond_other3.393.6081481
X-RAY DIFFRACTIONr_mcangle_it4.4576.4541850
X-RAY DIFFRACTIONr_mcangle_other4.4566.4561851
X-RAY DIFFRACTIONr_scbond_it4.5984.0291433
X-RAY DIFFRACTIONr_scbond_other4.5964.0311434
X-RAY DIFFRACTIONr_scangle_it6.3837.1662098
X-RAY DIFFRACTIONr_scangle_other6.3827.1672099
X-RAY DIFFRACTIONr_lrange_it8.75336.0453364
X-RAY DIFFRACTIONr_lrange_other8.63935.1273292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.95-2.0010.3161260.29526290.29627550.9370.9380.296
2.001-2.0560.281430.25125730.25227160.9480.9590.248
2.056-2.1150.261120.22324840.22525960.9590.9690.215
2.115-2.180.2361040.224900.20125940.9640.9750.187
2.18-2.2510.211240.17223380.17424620.9720.9820.156
2.251-2.330.1791220.15722910.15824130.980.9850.139
2.33-2.4180.2041240.15221610.15522850.9760.9870.132
2.418-2.5160.1741250.14621220.14822470.9830.9890.126
2.516-2.6280.205910.14320580.14521490.9760.990.124
2.628-2.7560.1911050.13519580.13820630.9770.990.119
2.756-2.9040.188860.12918420.13219280.9820.990.117
2.904-3.080.184950.14417750.14618700.9770.9870.135
3.08-3.2910.1971030.14616350.14917380.9740.9870.143
3.291-3.5530.159800.12715640.12816440.9860.990.129
3.553-3.890.181650.12914260.13114910.9790.9910.137
3.89-4.3460.152690.1112960.11213650.9870.9930.124
4.346-5.010.126640.09511490.09612130.9930.9950.111
5.01-6.1190.139450.1149890.11510340.9910.9930.133
6.119-8.5780.194440.1267720.138160.9760.9910.147
8.578-46.2770.13320.1354600.1354920.9890.9870.165
Refinement TLS params.Method: refined / Origin x: -20.0063 Å / Origin y: 8.5714 Å / Origin z: 56.8887 Å
111213212223313233
T0.046 Å20.0285 Å2-0.0376 Å2-0.0527 Å2-0.0052 Å2--0.0413 Å2
L1.1252 °20.1495 °2-0.3322 °2-1.0597 °2-0.2741 °2--0.9705 °2
S-0.0257 Å °0.1494 Å °0.1258 Å °-0.148 Å °-0.0039 Å °0.1458 Å °-0.1049 Å °-0.202 Å °0.0296 Å °
Refinement TLS groupSelection: ALL

+
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