PDB-7ayw: Crystal structure of a shortened IpgC variant in complex with 2H-...

ID or keywords:

Entry

Database: PDB / ID: 7ayw

Title

Crystal structure of a shortened IpgC variant in complex with 2H-isoindol-1-amine

Components

Chaperone protein IpgC

Keywords

CHAPERONE / IpgC / Dimer /

Shigella /

Mutant /

Magnesium /

Chlorine / 2H-isoindol-1-amine

Function / homology

Function and homology information

identical protein binding /

cytoplasm
Similarity search - Function

Biological species

Shigella flexneri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Gardonyi, M. / Heine, A. / Klebe, G.

Citation

Journal: To be published
Title: Crystal structure of a shortened IpgC variant in complex with 2H-isoindol-1-amine
Authors: Gardonyi, M. / Heine, A. / Klebe, G.

History

Deposition	Nov 13, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: 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 viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ayw.cif.gz	211.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7ayw.ent.gz	141.5 KB	Display	PDB format
PDBx/mmJSON format	7ayw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ay/7ayw ftp://data.pdbj.org/pub/pdb/validation_reports/ay/7ayw	HTTPS FTP

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Related structure data

Related structure data	6scbS S: Starting model for refinement
Similar structure data	5wqa-1 3m7d-d 7a8q-1 6rcw-1 1vlc-d 7a9v-1 6ftw-1 5wqa-2 6scb-d 5wxm-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Chaperone protein IpgC

B: Chaperone protein IpgC

hetero molecules

33.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration
dimer

Unit cell

Length a, b, c (Å)	56.791, 56.791, 162.092
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
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:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	ASN	ASN	(chain 'A' and (resid 9 through 28 or (resid 29...	A	A	9 - 20	1 - 12
1	2	LEU	LEU	CYS	CYS	(chain 'A' and (resid 9 through 28 or (resid 29...	A	A	25 - 63	17 - 55
1	3	TYR	TYR	TYR	TYR	(chain 'A' and (resid 9 through 28 or (resid 29...	A	A	65 - 72	57 - 64
1	4	MET	MET	ALA	ALA	(chain 'A' and (resid 9 through 28 or (resid 29...	A	A	74 - 77	66 - 69
1	5	TYR	TYR	ASP	ASP	(chain 'A' and (resid 9 through 28 or (resid 29...	A	A	80 - 148	72 - 140
2	6	GLY	GLY	ASN	ASN	(chain 'B' and (resid 9 through 12 or (resid 13...	B	B	9 - 20	1 - 12
2	7	LEU	LEU	CYS	CYS	(chain 'B' and (resid 9 through 12 or (resid 13...	B	B	25 - 63	17 - 55
2	8	TYR	TYR	TYR	TYR	(chain 'B' and (resid 9 through 12 or (resid 13...	B	B	65 - 72	57 - 64
2	9	MET	MET	ALA	ALA	(chain 'B' and (resid 9 through 12 or (resid 13...	B	B	74 - 77	66 - 69
2	10	TYR	TYR	ASP	ASP	(chain 'B' and (resid 9 through 12 or (resid 13...	B	B	80 - 148	72 - 140

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Protein , 1 types, 2 molecules AB

#1: Protein	Chaperone protein IpgC / Mass: 16310.492 Da / Num. of mol.: 2 / Mutation: M1_E9del, D152_E154del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipgC, ippI, CP0129 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2U4

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Non-polymers , 6 types, 195 molecules

#2: Chemical	ChemComp-F05 / 1H-isoindol-3-amine Mass: 132.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₈N₂
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.63 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 25% PEG 4000, 0.05 M TRIS (pH 7.0), 0.3 M magnesium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.78→50 Å / Num. obs: 29962 / % possible obs: 99.9 % / Redundancy: 7.5 % / B_iso Wilson estimate: 25.14 Å² / R_sym value: 0.07 / Net I/σ(I): 17.3
Reflection shell	Resolution: 1.78→1.88 Å / Num. unique obs: 4751 / CC_1/2: 1 / R_sym value: 0.784

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Processing

Software

Name	Version	Classification
XDS	1.02	data reduction
XDS	1.02	data scaling
PHASER	7.0.047	phasing
PHENIX	1.16	refinement
Coot	0.8.9	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6scb

6scb

Resolution: 1.78→47.06 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2284	1499	5 %	Random selection
R_work	0.1803	28462	-	-
obs	0.1827	29961	99.86 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 30.26 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→47.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2195	0	41	184	2420

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2320
X-RAY DIFFRACTION	f_angle_d	0.9741	3149
X-RAY DIFFRACTION	f_chiral_restr	0.0555	344
X-RAY DIFFRACTION	f_plane_restr	0.0071	427
X-RAY DIFFRACTION	f_dihedral_angle_d	16.1873	1375

LS refinement shell

Resolution: 1.78→1.84 Å

	R_factor	Num. reflection	% reflection
R_free	0.3127	133	-
R_work	0.2417	2525	-
obs	-	-	99.48 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.00436508997627	0.00162145232927	0.00933908279501	-0.000213907406306	0.00302080654949	0.0125548139983	-0.0871437095644	0.100481162842	0.0300509871813	0.0215481882849	0.0364883067786	0.156053997473	0.125740839062	0.351499126595	6.53306285795E-5	0.300469490522	0.040172055321	-0.0299893895532	0.263478548474	-0.000690085418229	0.259745964432	-17.214528568	15.367009693	3.4962446933
2	0.250823945618	0.0865006889348	-0.233310992467	0.198476740429	0.00525258576214	0.331697140929	-0.101906407286	0.158741019606	0.199672993544	0.121782059471	0.16901324192	-0.33344427935	-0.196186369973	-0.00174727237133	-0.00101124634333	0.359019635355	-0.00526813880924	-0.060496014516	0.203461195973	0.0254429153723	0.261409938392	-20.9760184283	31.3589587526	2.22576566917
3	0.0337889501705	-0.0116612481404	-0.0383083804815	0.034106687256	0.00128451077807	0.0425897027588	0.185946601951	-0.0835276050969	0.0163298863467	0.120724361785	-0.0581498646395	-0.305624945316	-0.273410267707	0.286034631486	-0.000466611780148	0.347086282359	-0.0725105133071	-0.0405096261123	0.377845324957	0.037703150233	0.246286861838	-17.6819499531	26.326956467	-5.78253727755
4	1.00456903183	-0.312755274863	-0.520494231881	0.509396549028	0.280238896478	0.318734961028	-0.0761846376132	0.131332845414	-0.0446555776876	-0.335797088429	-0.111474674654	0.0889291459968	-0.266281205493	-0.399510902106	-0.0895100830486	0.35391832885	0.0461626416447	-0.0572100687134	0.226292679857	0.00326544329181	0.222103672178	-25.481843186	28.5164812956	-7.91708742386
5	0.891556579519	0.733009372516	-0.467683797079	0.611827114574	-0.329815909957	0.451228098862	-0.325889130547	-0.121836836723	0.015695308319	0.0649635993079	0.0365622613458	0.351741074067	0.0793360889732	0.1186189295	-0.060963181336	0.429070494508	0.0119830875814	0.199527010416	0.306216582769	0.118286217168	0.83174236338	-9.15310013702	44.1562260635	34.5692307936
6	1.16818419235	0.02232152806	-0.478454751108	0.100153649602	0.426198450874	2.07744602407	-0.145824440208	-0.301581235683	-0.0711216705679	-0.412535823599	0.458472444418	0.856949646583	0.133244810724	0.0479257374777	0.154297659533	0.284221461666	0.0286580345578	-0.12461164977	0.231778862812	0.0329443578711	0.579168910072	-5.69363142226	42.4156880928	24.1467643643
7	0.0289347422044	-0.00249996863	-0.0154035425613	0.0482097916825	-0.0155066136445	0.0208354648444	-0.11965683617	-0.103185069117	0.486426680636	0.214196619363	0.0930972013836	-0.0807039873654	-0.466333578571	-0.116337604707	-0.000384413930203	0.232295236731	0.00732359914858	-0.0493512509602	0.2189662939	-0.0141435553287	0.258611212059	3.76385973665	41.3073893665	19.5787135469
8	0.151532987816	-0.0752483923625	0.0803935772125	0.0303794257382	-0.0448838508701	0.083868218931	0.191256494799	0.308778664835	0.17334727181	-0.176594647005	-0.216136428862	-0.108327461307	0.00194509459311	0.382256680137	-0.000104390495137	0.211964967849	0.0194609012277	-0.00452862994559	0.287316278446	0.00810485061456	0.25140110245	11.168753155	28.9212476279	18.6219127475
9	0.178382234556	0.0721319345379	0.228572423884	0.522341967749	0.0298968276743	0.284081216189	-0.0545223701246	-0.220509894569	0.0769249841173	0.0590173578804	0.0283959078015	0.0335041597299	0.0279775022062	-0.141101418416	2.01769269772E-5	0.161051696462	0.00445933813074	-0.00984774626786	0.190508792878	-0.0219625981399	0.170022158757	-0.686327786545	29.6694705181	19.9136467848
10	0.222424059035	0.559882440729	0.365205360267	2.13628688497	0.730633029804	0.62732491105	0.0429249281587	-0.0532503687473	0.0620619902906	0.511590359386	-0.0344189239534	-0.490459149255	0.215703149912	-0.0224870388394	-0.0153403234782	0.125690797066	0.0426117080343	-0.0177462629801	0.176133399265	-0.00390629767468	0.190557181903	4.30107082248	17.2419470772	18.2025706155
11	0.0244861941642	-0.0196772647314	0.0121914315684	0.0135314975251	-0.0105348282158	0.00508646013601	-0.23928797313	-0.177484423155	-0.0819990229776	0.189553102535	0.2130397873	0.23121438587	-0.262568924595	-0.145262965474	-0.0010941085332	0.181060851871	0.00787279774611	0.0314847027479	0.219784558714	-0.00624953770599	0.246963628055	-2.09137266957	13.9155787077	16.0118802819
12	0.663496972456	0.299978210389	0.1778500795	0.136897325357	0.0164782338901	0.52709482261	-0.0859347280678	0.0428613722502	-0.047326440882	-0.0706093841125	0.115791605611	0.0350027482391	-0.0158201624512	-0.042499895943	5.29098916144E-5	0.161062847136	-0.00834403208967	0.00293630642508	0.169069435568	-0.0159338451013	0.179178938637	-4.08537454714	18.3822235299	8.18124257888
13	1.40759866363	0.197756343844	-0.586235303539	0.426186778229	0.108017750635	0.339629389811	-0.305461359372	0.475470312758	-0.232545641806	-0.298120164222	0.0728167280322	-0.102278155054	-0.264895380471	-0.102428176398	-0.0646113235238	0.238901071682	-0.0205613378117	-0.0300317421878	0.256133400049	0.00294026370333	0.196233206246	-6.43761957811	15.956785226	-0.557170902087
14	0.332469262538	0.302925926863	0.0674311623308	0.962387430677	0.0487540353044	0.167897453549	-0.157058712272	0.500890322989	0.0654813300349	-0.628487127029	0.248899521389	-0.38994048027	-0.114466856012	0.420611882893	0.066077299334	0.293345076403	-0.0356594023559	0.0517772719685	0.341758345676	0.0119986215542	0.260610032553	1.76860254865	16.1918231035	-3.58747993845
15	0.222402818058	0.0267453752301	0.0657049506272	0.982254072165	-0.134306106697	0.403134345737	-0.125379509297	0.197116146555	-0.547923292207	-0.00638094326607	-0.0935169564119	-0.11475458941	0.0837312510201	-0.196096074401	-0.0831733691964	0.140494279227	-0.00861869715949	0.0400599356713	0.232390655083	-0.0363207150996	0.219623012566	-9.86106169491	21.8151943201	24.0211384003
16	0.665839078119	0.43158322619	0.720842034884	0.297779623269	0.376031255839	1.26087082998	0.191583041754	-0.496245328942	0.349755298729	0.067893579049	0.0631246793306	-0.394814415666	0.228881635604	0.00744224710443	0.0362850798613	0.273938298085	0.0769186723023	0.0556356265488	0.392628706035	0.0278017090203	0.643320146512	-15.5818623916	6.69509391055	24.8309037478
17	0.577235830867	0.0878385824549	-0.201996261739	0.409955852866	-0.185663475459	0.134305076964	-0.123837595194	-0.258432633032	-0.578129273053	-0.0521156847866	0.524697490389	0.594024675232	0.107971307704	-0.518171801889	0.100106969186	0.180202812187	-0.00969915396322	-0.0162695341683	0.303180222101	0.0562584604843	0.248371550393	-30.7981698782	12.7367498305	17.9942837685
18	1.27314677643	0.278416875254	0.005796729507	0.468086582557	0.0460011046599	0.427998334602	-0.153742366616	0.0475040920965	0.0622666609844	-0.00827575281836	0.0227722936542	-0.0841702496744	-0.692631633339	0.0895737269793	-0.0540773109392	0.250089596238	0.0219382516942	-0.0134072726193	0.278425716984	-0.000367528970353	0.128005949882	-22.8135532925	18.5517118456	20.9657064727
19	0.786730061992	0.0906356681934	0.410916638845	0.0680395993264	0.0396178298203	0.34898216429	-0.0931166486279	0.049244039406	0.057197483355	-0.00164837000736	-0.081251328402	-0.068131954711	-0.183711011606	-0.20467355044	-0.0043973357417	0.231350985888	0.00997257345902	-0.0419360092523	0.212372399492	-0.0176304418613	0.198720769965	-21.6821651004	24.3896824434	11.789925881

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 99 through 103 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 104 through 124 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 125 through 134 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 135 through 151 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 9 through 20 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 25 through 32 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 33 through 39 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 40 through 53 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 54 through 78 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 79 through 85 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 86 through 89 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 90 through 121 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 122 through 134 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 135 through 150 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 9 through 25 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 26 through 33 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 34 through 51 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 52 through 68 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 69 through 98 )

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 195 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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Yorodumi