PDB-7nl8: Crystal structure of a shortened IpgC variant in complex with 3-m...

ID or keywords:

Entry

Database: PDB / ID: 7nl8

Title

Crystal structure of a shortened IpgC variant in complex with 3-methylbenzohydrazide

Components

Chaperone protein IpgC

Keywords

CHAPERONE / IpgC / Dimer /

Shigella /

Mutant /

Magnesium /

Chlorine / 3-methylbenzohydrazide

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: 1.59 Å

Authors

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

Citation

Journal: To be published
Title: Crystal structure of a shortened IpgC variant in complex with 3-methylbenzohydrazide
Authors: Gardonyi, M. / Heine, A. / Klebe, G.

History

Deposition	Feb 22, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 2, 2022	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	7nl8.cif.gz	153.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7nl8.ent.gz	99.4 KB	Display	PDB format
PDBx/mmJSON format	7nl8.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/nl/7nl8 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/7nl8	HTTPS FTP

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Related structure data

Related structure data	6scbS S: Starting model for refinement
Similar structure data	7d7k-1 7m1y-2 4x2z-d 7d7k-2 7m1y-1 5mts-d 6j14-d 7d47-2 Search similar-shape structures by Omokage search (details) 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

B: Chaperone protein IpgC

hetero molecules

A: Chaperone protein IpgC

hetero molecules

defined by author&software
Evidence: gel filtration
33.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.530, 57.530, 159.520
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	ALA	ALA	ASP	ASP	(chain 'A' and (resid 23 through 28 or resid 30...	A	A	23 - 27	15 - 19
1	2	ALA	ALA	TYR	TYR	(chain 'A' and (resid 23 through 28 or resid 30...	A	A	30 - 40	22 - 32
1	3	TYR	TYR	TYR	TYR	(chain 'A' and (resid 23 through 28 or resid 30...	A	A	42 - 72	34 - 64
1	4	MET	MET	PHE	PHE	(chain 'A' and (resid 23 through 28 or resid 30...	A	A	74 - 97	66 - 89
1	5	ASP	ASP	VAL	VAL	(chain 'A' and (resid 23 through 28 or resid 30...	A	A	103 - 130	95 - 122
1	6	GLN	GLN	ASP	ASP	(chain 'A' and (resid 23 through 28 or resid 30...	A	A	132 - 148	124 - 140
2	1	ALA	ALA	ASP	ASP	(chain 'B' and (resid 23 through 28 or resid 30...	B	B	23 - 27	15 - 19
2	2	ALA	ALA	TYR	TYR	(chain 'B' and (resid 23 through 28 or resid 30...	B	B	30 - 40	22 - 32
2	3	TYR	TYR	TYR	TYR	(chain 'B' and (resid 23 through 28 or resid 30...	B	B	42 - 72	34 - 64
2	4	MET	MET	PHE	PHE	(chain 'B' and (resid 23 through 28 or resid 30...	B	B	74 - 97	66 - 89
2	5	ASP	ASP	VAL	VAL	(chain 'B' and (resid 23 through 28 or resid 30...	B	B	103 - 130	95 - 122
2	6	GLN	GLN	ASP	ASP	(chain 'B' and (resid 23 through 28 or resid 30...	B	B	132 - 148	124 - 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_E155del 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

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Non-polymers , 7 types, 188 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-45L / 3-methylbenzohydrazide Mass: 150.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₀N₂O
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.33 Å³/Da / Density % sol: 47.1 %
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: 0.91841 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: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.59→50 Å / Num. obs: 42121 / % possible obs: 99.6 % / Redundancy: 7.6 % / B_iso Wilson estimate: 22.42 Å² / CC_1/2: 1 / R_sym value: 0.045 / Net I/σ(I): 24.1
Reflection shell	Resolution: 1.59→1.67 Å / Num. unique obs: 6695 / CC_1/2: 0.932 / R_sym value: 0.8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6SCB

6scb

Resolution: 1.59→47.56 Å / SU ML: 0.1669 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.741
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.219	2103	5 %
R_work	0.1911	39965	-
obs	0.1925	42068	99.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.77 Å²

Refinement step

Cycle: LAST / Resolution: 1.59→47.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2118	0	41	178	2337

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0052	2285
X-RAY DIFFRACTION	f_angle_d	0.7188	3100
X-RAY DIFFRACTION	f_chiral_restr	0.0489	337
X-RAY DIFFRACTION	f_plane_restr	0.0054	410
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0762	1357

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.59-1.63	0.3041	136	0.2618	2579	X-RAY DIFFRACTION	97.8
1.63-1.67	0.2709	138	0.2463	2630	X-RAY DIFFRACTION	99.71
1.67-1.71	0.2701	139	0.231	2632	X-RAY DIFFRACTION	99.6
1.71-1.76	0.2935	137	0.2182	2612	X-RAY DIFFRACTION	99.85
1.76-1.82	0.2274	140	0.2184	2641	X-RAY DIFFRACTION	99.75
1.82-1.88	0.2247	140	0.1973	2658	X-RAY DIFFRACTION	99.79
1.88-1.96	0.2451	137	0.1932	2614	X-RAY DIFFRACTION	99.75
1.96-2.05	0.2586	141	0.1863	2661	X-RAY DIFFRACTION	99.82
2.05-2.16	0.2081	138	0.1869	2635	X-RAY DIFFRACTION	99.82
2.16-2.29	0.2156	140	0.1783	2675	X-RAY DIFFRACTION	99.79
2.29-2.47	0.2125	140	0.1773	2655	X-RAY DIFFRACTION	99.93
2.47-2.72	0.2035	142	0.1907	2707	X-RAY DIFFRACTION	99.89
2.72-3.11	0.2102	143	0.1946	2699	X-RAY DIFFRACTION	99.58
3.11-3.92	0.2135	143	0.1792	2725	X-RAY DIFFRACTION	99.41

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	1.51914430017	0.572281540235	-0.835461566279	0.297858423714	-0.834434752624	4.71881441859	0.0422379130183	-0.182858180976	-0.0881638433997	-0.463288562253	-0.181074983493	0.828240376345	-0.881141361477	-0.340288480662	0.081294570689	0.320196830022	0.158622764427	-0.111532301588	0.315462693265	-0.0557191363748	0.506099445463	-8.01870499144	40.6770653002	24.4462618103
2	0.0450057409902	-0.0661037632126	-0.0132533362584	0.0835475796689	0.0663263433227	0.0494450681106	-0.29180295511	-0.036994395872	0.125065656911	-0.0177382452885	0.0429687557621	0.433678204256	-0.551357336841	-0.581292513826	0.00203189994774	0.400285831585	0.0206203646907	-0.0527609759811	0.312513698102	-0.00917944241999	0.280841102361	2.66906133558	41.3391345461	20.8031210467
3	0.286624892893	-0.159553215263	0.155250973963	0.0368058925948	-0.0767072257516	0.0661425897498	-0.000607778117259	0.463357621774	0.129054290301	-0.0323660531679	-0.183358934473	-0.0173292741949	-0.0378935317076	0.35281643164	-1.35767196973E-5	0.197159962551	-0.00544436249708	-0.0146040374209	0.353085982324	0.0010023470448	0.231271981173	10.3514224176	30.0302533881	18.8575798725
4	0.555373635699	0.647418186316	0.518298661376	0.51793893252	0.614570044418	0.546146901454	0.000335000997404	-0.00147205245394	0.0729723972812	-0.0778824629268	-0.010559480614	-0.00257440660966	-0.0852042114239	0.0192867227554	6.04037789578E-5	0.171066808005	0.000159746439533	-0.0162811450959	0.243770322062	-0.0210780536227	0.202415498061	-1.30714066868	29.6826127678	19.7210462563
5	0.199226841131	0.016061996853	-0.060361825324	0.238956280959	0.218711202436	0.264475984216	-0.199493673385	-0.282961102035	0.0691404719232	0.422010199248	0.244646428967	-0.229829286851	0.102073728098	0.328234738473	-0.0606051974185	0.193877733603	0.0858679159992	-0.0448637038392	0.314076333712	-0.028620886792	0.26002236625	3.85037431826	17.240346494	17.2451147481
6	0.0648151344372	-0.0447226769726	0.00441064460684	0.15640043506	0.0599493980961	0.0502975568745	-0.0954316636111	0.267027213791	-1.37792677175	0.37294255011	0.128147219125	0.287081634249	0.263707270429	0.424708901813	-0.0010537777932	0.216327880893	0.0378922642493	0.01615438882	0.330072423087	-0.0484180278026	0.36933370056	-2.38907873751	14.4796264061	14.8895311857
7	0.433758487157	-0.341523521004	0.0246530278762	0.205120082174	-0.299954195755	1.51161123699	-0.0506551814486	0.177984464099	-0.26581687527	0.00351118471994	0.040433003121	-0.0224058760883	-0.024598924572	-0.0276513584145	-0.0484329347243	0.127486459054	-0.00471357675867	0.0116069799995	0.266637265686	-0.0453772083306	0.241076174915	-4.73354519828	20.0957626701	7.16513511856
8	0.21685745739	-0.617279273179	-0.363676965558	1.94410407054	1.27134320607	0.929021724529	0.230087389521	0.701444410193	-0.25857605662	-0.794829446014	-0.158975705978	0.167426657324	-0.115871236336	-0.360170108278	-0.0202419469733	0.141487234135	0.00230716702596	-0.0075861991131	0.410189000163	-0.0880113969347	0.289221179995	-5.97957675493	17.5428702109	-2.3315139775
9	0.559694433375	0.0835959581921	0.186194415333	1.66289101233	0.597820656151	0.836962840933	0.0504971137441	0.537785361311	-0.186248109314	-0.853577864283	-0.0117444860488	0.0333255709829	-0.114465373471	0.145221423012	-0.0300081752051	0.244813563016	0.0344814723718	0.0574237122881	0.391689540076	-0.0224276239478	0.325921105084	1.99393695738	18.3201521751	-4.43324272151
10	0.152971395005	0.146769637944	9.0879637098E-5	0.180819897573	-0.049560299596	0.0212164501256	-0.0715745900803	-0.701031796857	-0.444790708683	-0.185438277332	0.156703425766	-0.163508042006	0.359480112233	-0.0360957825859	0.00113437574395	0.184633064516	-0.0226618189719	0.0198698951813	0.345788487491	0.0291942430379	0.240559514577	-11.1852189284	23.6725215894	22.221741438
11	0.336472793758	-0.206537553788	-0.130479036634	0.38885034403	0.425186828544	0.512158728012	-0.68286105124	0.0922528828725	-0.361379974644	-0.0541767544469	-0.35368701986	0.296606461079	0.299759912843	-0.128119483521	-0.0310221242532	0.567524502112	0.182779755755	0.108649150933	0.496300798435	0.0598974983668	0.441872022359	-19.007009351	6.42099263621	23.5755238657
12	0.381799714729	0.169243739193	-0.335465943649	0.231566932227	-0.0456446050871	0.35084714323	-0.0664496834426	0.34776884452	-0.220193911016	-0.142252352477	-0.097337139144	0.0850607802451	0.284867932275	-0.339025817684	-0.000643050523292	0.316887118628	-0.0445121001741	0.00899340149309	0.338198485304	-0.0457257228278	0.21306011714	-32.551531288	14.7627099367	17.0389450791
13	0.0286735454255	-0.0601416153985	-0.0243150369737	0.124690001473	-0.204723845456	0.369176182185	0.0628020649127	-0.0755816417509	-0.0382000353599	-0.139706809837	-0.0329016865907	-0.16450873526	0.0722586868605	0.0844393455591	-5.64507521934E-5	0.222079249116	-0.0066754193514	0.0277793727181	0.259741072444	-0.0202743613088	0.210296753336	-23.8075768101	19.3450684429	19.8800967572
14	0.466657464177	-0.220770267936	-0.0593541268055	0.279292065767	-0.526173654195	0.647957728306	-0.0482954302181	-0.0380148896848	0.103751758793	-0.00748827577246	0.020070576242	-0.0342379227044	0.072337742581	-0.0189697605613	-4.88725050198E-5	0.215589417744	-0.00272796395173	0.00694587785329	0.233743037031	0.00385840930583	0.210983819256	-22.5353085947	25.4068276394	10.5639824077
15	2.92926710487	-0.404406084259	1.01470167765	0.103122243419	0.0311738189866	1.02281679042	0.337871154439	0.854680657246	-0.507524320832	0.188464192604	-0.222643885602	0.623579707844	0.310739277507	-0.00663508030263	0.00460567973389	0.45112421921	-0.0302268109344	0.0155501009088	0.291589871577	0.0335466790582	0.347470004484	-16.2861058736	16.87164487	2.12914397708
16	-0.0259816560273	-0.189753132235	-0.0382617334981	0.18067873223	0.0853191672889	0.485802429939	0.0578825515341	0.105834055839	0.0223831186055	-0.196753655386	-0.0297446991436	0.0684975520377	-0.263671570218	-0.0500484123798	-1.80448505804E-5	0.217134909457	-0.0204200882458	0.00744695692192	0.236128145842	0.0227294380788	0.213679527007	-21.214885312	32.0861723332	0.631992442913
17	0.0704524819996	0.0192544357612	-0.0180490047122	0.0214007953563	-0.0364218935117	0.0904081787483	0.191596853234	0.366128133698	0.0947481329175	-0.191143924856	0.0139417452767	-0.74834418377	-0.354719925031	0.418851989575	3.11212115704E-5	0.312386706118	-0.0157120887198	0.0245316428986	0.334808522668	0.00388956178221	0.255130473042	-17.6445476438	26.3281419522	-7.76870796929
18	0.293616273684	-0.00543986917862	-0.278431728391	0.184690089071	0.167897419668	0.236608371563	-0.0354570629324	0.035704069912	-0.182112126196	-0.237467439003	-0.0366272317763	0.255049551046	-0.17378081081	-0.543655730259	-0.00624887249808	0.351321157012	0.0459816877963	-0.0216868615831	0.268745560198	0.00617312588636	0.216489875825	-25.4864980236	27.7785689786	-9.10086057424

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 39 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 40 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 78 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 79 through 85 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 86 through 89 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 90 through 121 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 122 through 134 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 135 through 151 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 9 through 21 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 28 through 33 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 34 through 51 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 52 through 68 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 69 through 98 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 99 through 103 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 104 through 124 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 125 through 134 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 135 through 150 )

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