[English] 日本語
Yorodumi
- PDB-7owv: Crystal structure of IpgC in complex with a follow-up compound ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7owv
TitleCrystal structure of IpgC in complex with a follow-up compound based on J20
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Shigella / Mutant
Function / homology
Function and homology information


identical protein binding / cytoplasm
Similarity search - Function
Tetratricopeptide TPR-3 / Tetratricopeptide repeat / Type III secretion system, low calcium response, chaperone LcrH/SycD, subgroup / Type III secretion system, low calcium response, chaperone LcrH/SycD / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Chem-2IY / TRIETHYLENE GLYCOL / Chaperone protein IpgC
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Crystal structure of IpgC in complex with a follow-up compound based on J20
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionJun 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein IpgC
B: Chaperone protein IpgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1707
Polymers32,6212
Non-polymers5495
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-40 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.788, 57.788, 160.301
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASNASN(chain 'A' and (resid 14 through 20 or resid 23...AA14 - 206 - 12
12ALAALAPHEPHE(chain 'A' and (resid 14 through 20 or resid 23...AA23 - 5915 - 51
13PHEPHEASPASP(chain 'A' and (resid 14 through 20 or resid 23...AA61 - 6653 - 58
14ASNASNASNASN(chain 'A' and (resid 14 through 20 or resid 23...AA6961
15ASPASPTYRTYR(chain 'A' and (resid 14 through 20 or resid 23...AA71 - 7263 - 64
16METMETALAALA(chain 'A' and (resid 14 through 20 or resid 23...AA74 - 7766 - 69
17TYRTYRTYRTYR(chain 'A' and (resid 14 through 20 or resid 23...AA80 - 10472 - 96
18PROPROILEILE(chain 'A' and (resid 14 through 20 or resid 23...AA106 - 13198 - 123
19SERSERALAALA(chain 'A' and (resid 14 through 20 or resid 23...AA134 - 149126 - 141
210ALAALAASNASN(chain 'B' and ((resid 14 through 18 and (name N...BB14 - 206 - 12
211ALAALAPHEPHE(chain 'B' and ((resid 14 through 18 and (name N...BB23 - 5915 - 51
212PHEPHEASPASP(chain 'B' and ((resid 14 through 18 and (name N...BB61 - 6653 - 58
213ASNASNASNASN(chain 'B' and ((resid 14 through 18 and (name N...BB6961
214ASPASPTYRTYR(chain 'B' and ((resid 14 through 18 and (name N...BB71 - 7263 - 64
215METMETALAALA(chain 'B' and ((resid 14 through 18 and (name N...BB74 - 7766 - 69
216TYRTYRTYRTYR(chain 'B' and ((resid 14 through 18 and (name N...BB80 - 10472 - 96
217PROPROILEILE(chain 'B' and ((resid 14 through 18 and (name N...BB106 - 13198 - 123
218SERSERALAALA(chain 'B' and ((resid 14 through 18 and (name N...BB134 - 149126 - 141

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Chaperone protein IpgC


Mass: 16310.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipgC, ippI, CP0129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A2U4

-
Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-2IY / 3-(4-chlorophenyl)-5-methylsulfanyl-1~{H}-pyrazole-4-carbonitrile


Mass: 249.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8ClN3S
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30 % PEG 4000, 0.1 M TRIS pH 8, 0.3 M magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 42465 / % possible obs: 99.5 % / Redundancy: 9.64 % / Biso Wilson estimate: 26.71 Å2 / CC1/2: 0.999 / Rsym value: 0.049 / Net I/σ(I): 21.31
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 9.87 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 6615 / CC1/2: 0.893 / Rsym value: 0.821 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDS1.02data reduction
XDS1.02data scaling
PHASER7.0.047phasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6scb

6scb


Resolution: 1.59→36.53 Å / SU ML: 0.1787 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2123 5 %random selection
Rwork0.1879 40316 --
obs0.1895 42439 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 1.59→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 32 152 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592375
X-RAY DIFFRACTIONf_angle_d0.76413230
X-RAY DIFFRACTIONf_chiral_restr0.0497347
X-RAY DIFFRACTIONf_plane_restr0.0054437
X-RAY DIFFRACTIONf_dihedral_angle_d14.87281412
LS refinement shellResolution: 1.59→1.63 Å
RfactorNum. reflection% reflection
Rfree0.3237 131 -
Rwork0.2937 2473 -
obs--93.77 %
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)
18.703342714771.12827879011-0.8436248437656.442619390422.294540399145.10412844891-0.1123677386450.0309839899149-1.19757737166-0.362872570357-0.5635427924420.9180698338470.208779278764-1.399306485740.6116294892020.279887303517-0.08218793058290.02159490565850.610109745521-0.170684496540.517641748993-39.452073393513.8455663743-2.14869374479
25.006861005293.187561165843.945843163439.4238543764-0.5783993165254.413797601650.379995068016-0.3877980869320.365404166156-0.139066521194-0.5538256524791.38019220863-0.271748332566-1.474386645710.2018649068810.421831917250.0860245576175-0.01211364904720.472289866703-0.07909063133730.42212358131-34.786290421723.2514956266-5.72624551799
34.073512025252.887153207995.203404809015.58066860051.483124144268.10067622228-0.5198451004970.2727095963320.31981868072-0.3725949262910.1953328787360.0965830165442-0.8336619587220.08621940330180.2977773421630.377896890659-0.09480113655360.02381115872290.224704505626-0.003692342854550.231648984242-20.48427337123.7977894415-7.775378508
43.011159888541.276197886941.022973546414.299754164013.01934134795.134589789040.01640609912290.00197571831088-0.007750970257550.0289233464957-0.1020910622880.0991916555952-0.0215376191813-0.1849676147440.07886004693230.246686239767-0.02113324468060.01494814061360.167248583188-0.004048364820790.194944149464-27.092101134812.9570383053-7.28447971033
57.48920278468-3.52998922425-4.602523803458.370123012140.2348462890577.565713425080.173051426537-1.211527379940.4278070477730.3057340931970.0252841416668-0.475314335237-0.3110958755020.617776845729-0.1671075507130.224470114146-0.109395290776-0.0004212533815110.380131569229-0.05512281952960.315612721057-13.446941625712.3216218528-9.25579807686
67.93609673015-0.09053372975-5.220046784718.56563715718-2.597097684469.285905031590.0765361878665-0.433081474523-0.819796408562-0.6123859716780.000911747846511-1.1939879006-0.05755437859020.588611014784-0.07508211751910.37525874262-0.07205829543240.07943881318440.315379982633-0.004427484802310.43974018469-13.79740733145.192563858-11.833243949
75.69366448231.18260487921-0.7805217174222.32075297166-0.6364531053763.51088152786-0.0809192365560.105880867857-0.141152608203-0.3225928893980.101719616538-0.268736278418-0.1233878459370.0433791851701-0.02627852524250.285550336121-0.05793900761280.06158238746960.157128757448-0.02408717452950.249145009427-18.99719816865.83462088361-19.5489699556
85.37340049443-3.164914363664.683494462572.70851405497-1.89541467557.08350028675-0.1051480193490.697837583477-0.856154476916-0.7386775920020.374183446146-0.2422171565720.06710065849490.00401647778563-0.3339109051620.467493897031-0.1787409285720.1286686379590.313642949596-0.1084507450520.446409842772-18.94929862233.31908400629-28.8095090894
94.62289897183-4.475934686533.306072928747.03786329463-0.8159414735185.71211626454-0.05946678548641.34493695191-0.0992982088749-0.8590902055190.0711078411134-0.521853635678-0.4825933783360.459903611417-0.0003462390599730.553739939213-0.2035020690040.1062303503490.43964088194-0.008484233912820.415544176844-14.952279582410.9001515411-31.1408639517
103.437301255613.32236943622.221253785543.441506020241.187253681368.679615022050.639948370332-0.385752560225-0.06928295030550.616984746265-0.51719301346-0.5324472286750.316901673784-0.056490913908-0.1454707312020.395457843698-0.07661635403230.01085268045150.244520896340.04418957611050.286080961666-26.72360391942.03087315173-4.5609914889
118.05534965234-4.29959844601-1.408377937662.521877425191.275708295566.468074791820.4126030971370.2242617805240.623929076981-0.245897215835-0.838255996578-2.10704124877-0.4502005956210.8025204191880.4161077211690.501292863126-0.09465991660760.02893042267980.8664656524380.1412730494050.739964125043-15.7837983638-9.0010305473-2.38247148426
128.876286208442.48737341202-0.1813770617855.22823997357-0.4392279396856.69728977194-0.2581195127030.199237164758-0.581641714082-0.4481482635220.0242147720817-0.3507343143860.7146039635030.1116102443330.2177447089010.4266388508130.007587700871540.08538198804880.273239609452-0.02705031325250.227841763658-28.9649593194-20.9335179017-9.57783780824
133.506778509794.37062495005-2.44383080017.27429583935-1.669345669749.107860714250.06350721972650.2253429940410.1042506047820.130574283067-0.0305918839601-0.129251638633-0.02879618243780.187024500588-0.06957446444650.2504631440830.02103111055230.02868800541640.1803389451190.008681941349550.196552626486-29.2396644694-10.8764864976-6.70394929687
146.28269164109-0.3558337992741.961063441624.01332797331-2.154861970914.38297162460.0614772917636-0.224006772372-0.0249278499346-0.0226392271184-0.0668076510440.1734648210070.187024946506-0.2162637103180.01414612568490.276482802792-0.01507742436010.01189097676320.210015974155-0.02089160504320.175536204476-33.3676971152-6.79735601544-16.0970865167
153.44144376864.819700059782.462623935659.10900094842.154984326282.46338762141-0.6814926618251.27517033385-1.28043050095-0.8551631821151.58828793629-1.247925030380.225822045193.02082811163-1.090102114640.5183461945090.01096402176950.08779833139110.709055095226-0.01227502680570.425157466984-23.1627227727-6.91348236706-23.6864295964
165.60060435357-2.14263511081-3.578697535664.51220944153-0.1957519240123.356080654270.0266583137784-0.05953921356150.223073097541-0.120041266640.07569125108140.441611097693-0.40540607366-0.391760924371-0.1117477058310.3268358917730.000742437523133-0.06293183393620.290711874723-0.005379208005530.277168983243-38.3436287699-2.74315387693-25.9126583657
173.88515018306-0.929868377891-6.003334900167.953674024861.850326748219.39999065922-0.01163924767460.6523524205051.17623820914-0.3404735272140.329987761287-0.178319347636-1.06732394484-0.302798632605-0.2161951208470.409067908882-0.0191281131886-0.04457848304650.401526896350.03473100657060.32383247486-32.2507627152-1.54553082215-33.7409065733
189.26132726671-5.8653931829-3.825881639823.937533790232.214214676435.6045156610.2272590741910.680686081772-0.249086664269-0.254194969706-0.3298333485960.2856384100060.478007563072-0.507426709110.08621328955790.303308652963-0.0241599939281-0.02428707080030.368078108197-0.03429003185490.301293799277-36.6541203835-8.6531279826-35.9588508245
196.777109473063.862014178140.8947068809216.123685118450.8596556425486.38276538176-0.00557224022798-0.0561108117069-1.58191627481-2.088336750620.03302338676991.131157328241.5112465549-0.7416431299990.06652597204470.750801846414-0.13203553616-0.1521271861430.2654839064980.101444235620.966231736168-38.24359799094.564514213394.11163928087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 85 )
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 89 )
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 121 )
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 134 )
9X-RAY DIFFRACTION9chain 'A' and (resid 135 through 151 )
10X-RAY DIFFRACTION10chain 'B' and (resid 9 through 20 )
11X-RAY DIFFRACTION11chain 'B' and (resid 23 through 33 )
12X-RAY DIFFRACTION12chain 'B' and (resid 34 through 51 )
13X-RAY DIFFRACTION13chain 'B' and (resid 52 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 98 )
15X-RAY DIFFRACTION15chain 'B' and (resid 99 through 103 )
16X-RAY DIFFRACTION16chain 'B' and (resid 104 through 124 )
17X-RAY DIFFRACTION17chain 'B' and (resid 125 through 134 )
18X-RAY DIFFRACTION18chain 'B' and (resid 135 through 150 )
19X-RAY DIFFRACTION19chain 'A' and (resid 14 through 23 )

+
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://pdbjlvh1.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