PDB-7tba: Pentraxin - ligand complex

ID or keywords:

Entry

Database: PDB / ID: 7tba

Title

Pentraxin - ligand complex

Components

C-reactive protein

Keywords

IMMUNE SYSTEM / Inflammation / Inhibitor / Complex

Function / homology

Function and homology information

regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / Classical antibody-mediated complement activation / low-density lipoprotein particle receptor binding / negative regulation of macrophage derived foam cell differentiation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Shing, K.S.C.T. / Morton, C.J. / Parker, M.W.

Funding support

1items

Citation

Journal: Embo Mol Med / Year: 2023
Title: A novel phosphocholine-mimetic inhibits a pro-inflammatory conformational change in C-reactive protein.
Authors: Zeller, J. / Cheung Tung Shing, K.S. / Nero, T.L. / McFadyen, J.D. / Krippner, G. / Bogner, B. / Kreuzaler, S. / Kiefer, J. / Horner, V.K. / Braig, D. / Danish, H. / Baratchi, S. / Fricke, M. ...

History

Deposition	Dec 21, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 3, 2023	Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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 / _citation.year / _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
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7tba.cif.gz	2.3 MB	Display	PDBx/mmCIF format
PDB format	pdb7tba.ent.gz	1.9 MB	Display	PDB format
PDBx/mmJSON format	7tba.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7tba_validation.pdf.gz	3.9 MB	Display	wwPDB validaton report
Full document	7tba_full_validation.pdf.gz	3.9 MB	Display
Data in XML	7tba_validation.xml.gz	148.8 KB	Display
Data in CIF	7tba_validation.cif.gz	185 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tb/7tba ftp://data.pdbj.org/pub/pdb/validation_reports/tb/7tba	HTTPS FTP

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Related structure data

Related structure data	1b09S S: Starting model for refinement
Similar structure data	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	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: C-reactive protein

B: C-reactive protein

C: C-reactive protein

D: C-reactive protein

E: C-reactive protein

F: C-reactive protein

G: C-reactive protein

H: C-reactive protein

I: C-reactive protein

J: C-reactive protein

K: C-reactive protein

L: C-reactive protein

M: C-reactive protein

N: C-reactive protein

O: C-reactive protein

P: C-reactive protein

Q: C-reactive protein

R: C-reactive protein

S: C-reactive protein

T: C-reactive protein

hetero molecules

468 kDa, 20 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: C-reactive protein

B: C-reactive protein

C: C-reactive protein

D: C-reactive protein

E: C-reactive protein

hetero molecules

defined by author
Evidence: SAXS
117 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: C-reactive protein

G: C-reactive protein

H: C-reactive protein

I: C-reactive protein

J: C-reactive protein

hetero molecules

defined by author
117 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

K: C-reactive protein

L: C-reactive protein

M: C-reactive protein

N: C-reactive protein

O: C-reactive protein

hetero molecules

defined by author
117 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

P: C-reactive protein

Q: C-reactive protein

R: C-reactive protein

S: C-reactive protein

T: C-reactive protein

hetero molecules

defined by author
117 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.568, 98.172, 160.400
Angle α, β, γ (deg.)	89.080, 89.760, 87.480
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 1 - 206 / Label seq-ID: 1 - 206

#1: Protein	C-reactive protein Mass: 23068.039 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRP, PTX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02741
#2: Chemical	ChemComp-XQY / [3-(dibutylamino)propyl]phosphonic acid Mass: 251.303 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₁₁H₂₆NO₃P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Ca
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.28 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100mM Tris pH 9.0, 10% PEG 4000, 50mM lithium chloride, 200mM magnesium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 6, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 3.5→41.54 Å / Num. obs: 184033 / % possible obs: 95.9 % / Redundancy: 3.4 % / CC_1/2: 0.947 / Net I/σ(I): 4.63
Reflection shell	Resolution: 3.5→3.625 Å / Num. unique obs: 5362 / CC_1/2: 0.635

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHENIX	1.19.2_4158	refinement
PDB_EXTRACT	3.27	data extraction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1B09

1b09

Resolution: 3.5→41.54 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2598	1989	3.72 %
R_work	0.2124	51478	-
obs	0.2142	53467	95.95 %

Solvent computation

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

Displacement parameters

B_iso max: 211.81 Å² / B_iso mean: 62.4932 Å² / B_iso min: 17.39 Å²

Refinement step

Cycle: final / Resolution: 3.5→41.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	32640	0	840	0	33480
B_iso mean	-	-	77.77	-	-
Num. residues	-	-	-	-	4120

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	2	B	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	3	C	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	4	D	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	5	E	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	6	F	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	7	G	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	8	H	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	9	I	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	10	J	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	11	K	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	12	L	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	13	M	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	14	N	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	15	O	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	16	P	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	17	Q	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	18	R	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	19	S	12700	X-RAY DIFFRACTION	2.622	TORSIONAL
1	20	T	12700	X-RAY DIFFRACTION	2.622	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.5-3.59	0.3066	140	0.2713	3673	3813	96
3.59-3.68	0.3052	152	0.2676	3671	3823	97
3.68-3.79	0.3305	143	0.2762	3751	3894	96
3.79-3.92	0.3328	136	0.2669	3602	3738	95
3.92-4.05	0.294	145	0.251	3665	3810	95
4.06-4.22	0.292	130	0.2259	3641	3771	95
4.22-4.41	0.2834	140	0.203	3641	3781	95
4.41-4.64	0.2275	142	0.1875	3713	3855	96
4.64-4.93	0.2162	137	0.1803	3671	3808	96
4.93-5.31	0.2679	145	0.1808	3697	3842	97
5.31-5.84	0.2459	152	0.193	3722	3874	97
5.84-6.69	0.2006	140	0.1919	3728	3868	97
6.69-8.41	0.2763	152	0.1943	3688	3840	97
8.41-41.54	0.1802	135	0.1748	3615	3750	94

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	0.8405	-0.302	0.2007	0.9269	-0.1425	0.8386	-0.0174	0.1515	-0.0099	-0.0695	-0.0163	-0.0516	0.0442	0.2757	0	0.3613	-0.0773	-0.0299	0.2581	-0.0198	0.3899	-12.7764	19.6544	-41.6108
2	1.5323	0.9955	1.0532	1.3144	0.4433	0.8003	-0.0355	-0.0644	-0.0573	0.0462	0.0606	-0.0262	-0.0716	0.2053	-0.0001	0.4176	0.0213	-0.0302	0.4505	0.0499	0.2695	-7.0581	24.5198	-5.2559
3	1.317	0.5867	-0.6142	0.7138	-0.7394	0.9266	0.0172	-0.0278	0.0408	0.1494	-0.0058	-0.1013	-0.1688	-0.2501	0	0.3525	0.0074	-0.065	0.2295	-0.0281	0.3663	-2.6449	60.8331	0.445
4	0.7227	0.2226	-0.0305	0.8129	-0.3534	1.0372	-0.0008	0.1967	0.0685	0.1251	0.009	-0.02	-0.1345	-0.1104	-0	0.2149	0.0352	0.0311	0.3081	0.0253	0.4129	-6.1891	78.5552	-31.9969
5	1.2186	0.7548	-0.3114	1.8183	0.2872	0.8288	-0.0333	0.1112	-0.0239	-0.1622	0.0839	-0.041	0.0439	-0.0844	0	0.433	-0.0438	0.0291	0.3016	0.0196	0.2823	-11.9479	52.8953	-58.0839
6	1.1085	-0.539	0.7759	1.2023	0.3005	1.2203	0.0101	0.0897	-0.1006	-0.0141	-0.1433	0.1491	-0.0762	-0.0679	0.0001	0.3011	-0.0801	-0.0168	0.411	-0.0151	0.4291	-39.2718	41.7215	-8.0146
7	1.0334	0.2846	-0.0215	1.3093	-0.7857	0.4894	0.1024	0.2112	-0.0777	-0.1314	-0.0532	-0.0415	0.0321	0.0759	-0.0001	0.242	0.051	0.0108	0.4133	0.0206	0.2722	-43.8246	64.6784	-36.6888
8	0.7912	-0.4758	0.4354	1.2669	0.5765	1.5416	0.1281	-0.0432	0.1294	0.226	-0.0444	0.1524	-0.1415	-0.0076	-0.0001	0.2277	-0.0187	0.0861	0.2304	0.0224	0.2745	-38.6971	99.4491	-24.5114
9	0.8587	-0.2984	-0.1855	0.9316	-1.0485	1.5182	-0.0293	-0.0689	-0.0082	0.124	0.0124	-0.0994	-0.1839	0.1709	-0.0001	0.4592	0.0501	-0.0119	0.4467	-0.0257	0.3078	-29.9169	97.8702	11.3716
10	0.2919	0.1754	-0.3698	2.0353	0.9442	1.128	-0.0484	0.0104	-0.0129	0.3957	0.027	-0.0022	0.1616	-0.1078	0.0001	0.3199	-0.0062	-0.0023	0.4089	0.03	0.3242	-31.8968	62.2362	21.9547
11	0.8706	-0.0554	-0.6146	1.3699	-0.9723	1.3894	0.0896	0.0522	0.0311	0.4517	-0.1981	-0.0607	-0.2138	0.2791	0.0031	0.5264	-0.0907	-0.0128	0.2597	-0.0236	0.4631	-0.1308	129.9529	67.5871
12	0.8504	-0.225	-0.8478	1.3642	0.7708	1.1912	0.0402	0.0714	0.1015	0.0981	0.0043	-0.1829	-0.0419	0.1046	-0	0.346	-0.0445	0.0093	0.4981	0.09	0.2828	8.1847	123.8846	31.9423
13	0.041	0.2006	-0.0855	0.9424	-0.2795	0.9505	-0.0308	0.3076	-0.1059	-0.0637	0.1634	-0.1361	0.2237	-0.0533	0.0341	0.2129	-0.032	0.1278	0.4973	-0.0126	0.4866	8.4882	87.2281	26.5212
14	0.5242	-0.4376	-0.2816	0.896	-0.4275	1.3334	-0.0572	-0.2083	-0.279	-0.021	-0.0908	-0.1957	0.0578	-0.0552	-0.0013	0.3151	-0.007	0.0475	0.2647	0.0425	0.5326	1.8726	70.7469	59.1055
15	1.5025	-1.184	-0.4491	1.9183	0.9659	0.5103	0.0008	-0.2204	0.0968	0.0239	0.0477	-0.0991	-0.1547	-0.0081	-0	0.4037	-0.004	-0.0361	0.4456	0.0258	0.2644	-4.2512	97.2097	84.3915
16	0.2764	0.0604	0.2673	0.8081	-0.6923	0.9247	0.1947	-0.1607	0.0937	0.237	0.1433	0.1411	-0.7721	-0.2775	0.1058	0.8611	0.0963	0.1048	0.2444	-0	0.4183	-36.855	142.8991	73.1694
17	0.7765	0.3945	-1.0378	2.0314	-0.3229	1.4789	0.1744	-0.0149	0.0262	0.0307	-0.0248	0.0687	-0.0719	-0.1653	-0	0.3579	0.015	-0.014	0.5177	0.0316	0.2754	-42.6499	119.991	101.7593
18	0.4388	-0.0307	-0.3993	0.9363	0.5154	0.6512	-0.0166	-0.074	0.0525	-0.1726	-0.0418	0.0441	-0.0412	-0.0664	0.0001	0.2813	0.0188	0.0107	0.2997	0.0401	0.2877	-38.5878	85.1394	89.5263
19	1.0099	0.7458	-0.2309	1.1479	-0.1592	1.1787	-0.0529	0.0913	0.0446	0.0045	0.0831	-0.1072	0.1656	-0.188	-0.0001	0.3495	0.0039	0.0006	0.4876	0.0088	0.271	-30.4534	86.5025	53.4037
20	0.6761	0.4312	0.1704	1.5344	0.4234	0.7215	0.0043	0.2375	0.416	-0.2791	-0.134	-0.0887	-0.3294	-0.055	-0.0019	0.4916	0.0841	-0.0252	0.3817	-0.009	0.3295	-29.9296	122.1503	43.1688

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 1 through 206)	A	1 - 206
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 1 through 206)	B	1 - 206
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 1 through 206)	C	1 - 206
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 1 through 206)	D	1 - 206
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 1 through 206)	E	1 - 206
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 1 through 206)	F	1 - 206
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 1 through 206)	G	1 - 206
8	X-RAY DIFFRACTION	8	(chain 'H' and resid 1 through 206)	H	1 - 206
9	X-RAY DIFFRACTION	9	(chain 'I' and resid 1 through 206)	I	1 - 206
10	X-RAY DIFFRACTION	10	(chain 'J' and resid 1 through 206)	J	1 - 206
11	X-RAY DIFFRACTION	11	(chain 'K' and resid 1 through 206)	K	1 - 206
12	X-RAY DIFFRACTION	12	(chain 'L' and resid 1 through 206)	L	1 - 206
13	X-RAY DIFFRACTION	13	(chain 'M' and resid 1 through 206)	M	1 - 206
14	X-RAY DIFFRACTION	14	(chain 'N' and resid 1 through 206)	N	1 - 206
15	X-RAY DIFFRACTION	15	(chain 'O' and resid 1 through 206)	O	1 - 206
16	X-RAY DIFFRACTION	16	(chain 'P' and resid 1 through 206)	P	1 - 206
17	X-RAY DIFFRACTION	17	(chain 'Q' and resid 1 through 206)	Q	1 - 206
18	X-RAY DIFFRACTION	18	(chain 'R' and resid 1 through 206)	R	1 - 206
19	X-RAY DIFFRACTION	19	(chain 'S' and resid 1 through 206)	S	1 - 206
20	X-RAY DIFFRACTION	20	(chain 'T' and resid 1 through 206)	T	1 - 206

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