[English] 日本語
Yorodumi
- PDB-7k9r: Cryptococcus neoformans Hsp90 nucleotide binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k9r
TitleCryptococcus neoformans Hsp90 nucleotide binding domain
ComponentsHsp90-like protein
KeywordsCHAPERONE / Crytococcus neoformans / HSP90 ATP-binding
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKuntz, D.A. / Kenney, T. / Prive, G.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI120958 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Fungal-Selective Resorcylate Aminopyrazole Hsp90 Inhibitors: Optimization of Whole-Cell Anticryptococcal Activity and Insights into the Structural Origins of Cryptococcal Selectivity.
Authors: Marcyk, P.T. / LeBlanc, E.V. / Kuntz, D.A. / Xue, A. / Ortiz, F. / Trilles, R. / Bengtson, S. / Kenney, T.M.G. / Huang, D.S. / Robbins, N. / Williams, N.S. / Krysan, D.J. / Prive, G.G. / ...Authors: Marcyk, P.T. / LeBlanc, E.V. / Kuntz, D.A. / Xue, A. / Ortiz, F. / Trilles, R. / Bengtson, S. / Kenney, T.M.G. / Huang, D.S. / Robbins, N. / Williams, N.S. / Krysan, D.J. / Prive, G.G. / Whitesell, L. / Cowen, L.E. / Brown, L.E.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Hsp90-like protein
B: Hsp90-like protein
C: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0265
Polymers71,9553
Non-polymers712
Water7,368409
1
A: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0212
Polymers23,9851
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0212
Polymers23,9851
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hsp90-like protein


Theoretical massNumber of molelcules
Total (without water)23,9851
Polymers23,9851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.230, 80.260, 149.890
Angle α, β, γ (deg.)90.000, 92.319, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-301-

CL

21B-421-

HOH

-
Components

#1: Protein Hsp90-like protein


Mass: 23985.100 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J9VVA4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1M LiCL, Hepes pH7, 20-25% PEG 6K, 10-20% DMSO / PH range: 6.5-7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→29.95 Å / Num. obs: 48718 / % possible obs: 85.22 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03001 / Net I/σ(I): 16.76
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.14 / Num. unique obs: 4717 / CC1/2: 0.71 / % possible all: 83.4

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CJI

6cji


Resolution: 1.95→29.95 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2004 3414 3.64 %
Rwork0.168 90411 -
obs0.1692 93825 83.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.99 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 2 409 5397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01025139
X-RAY DIFFRACTIONf_angle_d1.17866938
X-RAY DIFFRACTIONf_chiral_restr0.0798797
X-RAY DIFFRACTIONf_plane_restr0.0081887
X-RAY DIFFRACTIONf_dihedral_angle_d14.84131928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.27861160.26813070X-RAY DIFFRACTION68.46
1.98-2.010.3051580.24914111X-RAY DIFFRACTION90.44
2.01-2.040.29591360.25353820X-RAY DIFFRACTION87.04
2.04-2.05X-RAY DIFFRACTION5
2.09-2.110.2698630.23621360X-RAY DIFFRACTION73.73
2.11-2.150.27371530.22224465X-RAY DIFFRACTION98.03
2.15-2.190.20881620.20134414X-RAY DIFFRACTION97.97
2.19-2.230.29851600.20114091X-RAY DIFFRACTION90.27
2.23-2.280.2853870.2042504X-RAY DIFFRACTION54.98
2.28-2.330.2311740.18354366X-RAY DIFFRACTION99.19
2.33-2.390.21791620.18534493X-RAY DIFFRACTION99.42
2.39-2.460.24621830.18684505X-RAY DIFFRACTION99.36
2.46-2.530.22281550.17974398X-RAY DIFFRACTION98.7
2.53-2.610.21551670.18344505X-RAY DIFFRACTION97.66
2.61-2.70.2752190.2178370X-RAY DIFFRACTION8.48
2.7-2.810.19541740.18714418X-RAY DIFFRACTION98.31
2.81-2.940.21371720.18084438X-RAY DIFFRACTION98.5
2.94-3.10.17941620.1694491X-RAY DIFFRACTION98.73
3.1-3.290.18311690.15724460X-RAY DIFFRACTION98.78
3.29-3.540.20061620.15024384X-RAY DIFFRACTION98.06
3.54-3.90.17441710.14474351X-RAY DIFFRACTION96.38
3.9-4.460.14571650.12944458X-RAY DIFFRACTION98.28
4.46-5.610.17511630.13724484X-RAY DIFFRACTION99.51
5.62-29.950.18971810.16684436X-RAY DIFFRACTION98.67
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)
15.632026806281.16989167363-0.442332323833.44950197027-0.04458675278792.924505908640.00983440741550.1634606417880.118946404346-0.09449422038480.071203330718-0.00624890804659-0.08584003447230.13732170742-0.04903122077930.155728642469-0.01472357092510.01761224100890.1650136467660.01265172906820.13940267961612.14385630023.5995260259134.1569618869
22.29681402402-0.2258950004310.5059436288982.80214179239-0.8161131495934.629636956090.042743366995-0.1705065525370.1122385683250.4478997470790.07397414297720.225591627173-0.172822500259-0.0913146826565-0.09511210363310.200282185928-0.01667959729610.06377670735090.119870285503-0.003885434824190.201644151542-0.1745284364961.3747254436753.6697245751
32.652823185450.00111774253488-0.8516895305282.779751743630.5615899261283.40444801358-0.009842562072920.08789181642310.00257080289125-0.04717328780440.0880756369271-0.1181625598140.09507955230940.185487223138-0.09031985904480.132063836755-0.02144520157350.003790819535040.1132658221810.01768669884820.1703883296897.663474227690.72427947803541.1392339293
42.980407701380.365626603928-1.266290189241.88173277946-0.3297176782032.263384072620.08875082265880.1543510641040.1830630790070.05186375990740.04837396666370.222421255895-0.188129290159-0.187365762446-0.1122643308930.1791040404060.03421983691560.01007164678510.09668515170760.01058652665310.191605664831-1.232021311156.7648067233343.7303558063
53.44346292211-0.0328305771127-1.106595697214.822748414330.7792618995765.00322230551-0.08132492677170.199838722662-0.1439421073520.093938266255-0.05569317244310.2359637212970.199154936441-0.09373255539160.138393901870.264733405812-0.009056876648690.06023118569660.2267927125350.001801256027920.125862675755-1.02841847901-21.185414709567.5133510685
62.295942558531.59843654425-0.2585165505495.38162142118-0.8281444643052.599401004770.01382802508130.0443923941297-0.118448288067-0.0941709032383-0.300122089329-0.5431652813330.08553337930310.2877150112170.2043873063030.1249716692210.06572821356470.00640483330440.2468031064950.02188282443230.18007285924914.8006833563-19.151047429153.6917586191
75.30050032465-1.1044780392-0.4685457184273.48169517942-0.7403721627362.661945726870.140701499940.126308454297-0.02678831169880.13301440602-0.03848196427590.381150909023-0.104449617276-0.286021975001-0.09046139879930.1930997244130.006819126502150.02067633177480.2049858417770.01001633653350.166254292436-0.262818597636-12.837375646660.4449363601
82.1467812716-0.46506298681-0.8995318849463.110344165940.2949249306862.50201369526-0.05253415304240.0017305272338-0.178224220032-0.0184220417678-0.139098316602-0.08397254220720.1412242977710.07419151450090.1717666462880.1424298856330.0347367146278-0.02279847587070.1783763058680.03587772265830.16379739359710.5098382916-25.165027645659.1081640818
92.479728824830.942506243365-1.107195384792.25417951866-0.6165679027933.85823317167-0.06675344320890.000106024583954-0.319803886549-0.176728672317-0.126247799492-0.352699752950.1744769730980.4635574641510.0755445680740.1352574459380.0145126140622-0.009435034561110.254873914657-0.01270219906970.2064270657960.82801895226-30.344005016520.0675136304
102.89337156612-0.135651437567-0.9267559572324.4812328065-0.2580960190562.430648425690.04757940551710.0322421387845-0.401137084865-0.246066401338-0.160524608331-0.02262992756990.1622774170680.165618011510.111944194040.217060394559-0.01285452846690.007007374804370.264805742364-0.03890624162410.238236302504-2.67819724987-31.575319973112.6461422565
115.762936235152.126648574090.1722841257972.812920918361.193040954726.552825426210.240750339354-0.334400370732-0.1690988815150.114292368297-0.2678540504810.007522310969120.1648684358880.2687535044580.03674051445810.208338492587-0.0157336779984-0.04274852474530.274166626097-0.004876410101070.216986375683-0.566764832916-23.50058823733.0203087517
122.376967691870.884319473778-1.395537179192.40165766383-1.520148887294.89452377593-0.02939802376330.0875996283824-0.163360941184-0.209686233548-0.0726748348075-0.06344037752240.1372090416580.03989915886750.07392043764850.148811786011-0.00415180238309-0.006507601688060.198309268544-0.0570060699040.149389862968-4.58656533214-28.126375874313.4678600606
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 26 )AA-1 - 261 - 27
22chain 'A' and (resid 27 through 69 )AA27 - 6928 - 70
33chain 'A' and (resid 70 through 139 )AA70 - 13971 - 144
44chain 'A' and (resid 140 through 211 )AA140 - 211145 - 216
55chain 'B' and (resid -1 through 26 )BD-1 - 261 - 28
66chain 'B' and (resid 27 through 79 )BD27 - 7929 - 82
77chain 'B' and (resid 80 through 122 )BD80 - 12283 - 126
88chain 'B' and (resid 123 through 211 )BD123 - 211127 - 216
99chain 'C' and (resid 2 through 62 )CG2 - 621 - 61
1010chain 'C' and (resid 63 through 93 )CG63 - 9362 - 93
1111chain 'C' and (resid 94 through 122 )CG94 - 12294 - 122
1212chain 'C' and (resid 123 through 211 )CG123 - 211123 - 212

+
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