PDB-5ce0: Crystal structure of conserpin with Z-mutation

ID or keywords:

Entry

Database: PDB / ID: 5ce0

Title

Crystal structure of conserpin with Z-mutation

Components

Native conserpin with Z-variant (E342K)

Keywords

hydrolase inhibitor / Serine Protease Inhibitor / Aggregation Resistant / Consensus Design / Stability / Z-variant

Function / homology

Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Porebski, B.T. / McGowan, S. / Keleher, S. / Buckle, A.M.

Citation

Journal: Sci Rep / Year: 2016
Title: Smoothing a rugged protein folding landscape by sequence-based redesign.
Authors: Porebski, B.T. / Keleher, S. / Hollins, J.J. / Nickson, A.A. / Marijanovic, E.M. / Borg, N.A. / Costa, M.G. / Pearce, M.A. / Dai, W. / Zhu, L. / Irving, J.A. / Hoke, D.E. / Kass, I. / ...

History

Deposition	Jul 6, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 5, 2016	Group: Database references
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ce0.cif.gz	287.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5ce0.ent.gz	232.4 KB	Display	PDB format
PDBx/mmJSON format	5ce0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ce0_validation.pdf.gz	425.8 KB	Display	wwPDB validaton report
Full document	5ce0_full_validation.pdf.gz	429.1 KB	Display
Data in XML	5ce0_validation.xml.gz	27.5 KB	Display
Data in CIF	5ce0_validation.cif.gz	39 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ce/5ce0 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/5ce0	HTTPS FTP

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Related structure data

Related structure data	5cdxSC 5cdzC 5ce2 PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5myd-1 2riw-d 5twl-d 5myf-d 3pve-d 1qu0-1 2y24-d 4bqo-2 4f19-d 2v3q-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Native conserpin with Z-variant (E342K)

B: Native conserpin with Z-variant (E342K)

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

1

A: Native conserpin with Z-variant (E342K)

defined by author&software
42.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Native conserpin with Z-variant (E342K)

defined by author&software
42.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.220, 150.270, 51.015
Angle α, β, γ (deg.)	90.00, 94.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Native conserpin with Z-variant (E342K) Mass: 42578.398 Da / Num. of mol.: 2 / Mutation: E313K Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.29 % / Description: Large, rectangular crystals
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystals appeared within 5 days in 20% (v/v) polyethylene glycol (PEG) 3350, 0.01 M Bis Tris and 0.2 M Magnesium chloride (hexahydrate)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 30, 2013
Radiation	Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.3→37.57 Å / Num. obs: 32616 / % possible obs: 99.64 % / Redundancy: 7.7 % / R_merge(I) obs: 0.1474 / Net I/σ(I): 30.83

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5CDX

5cdx

Resolution: 2.3→37.568 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2294	1729	5.31 %	Random selection
R_work	0.2012	-	-	-
obs	0.2027	32565	99.49 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→37.568 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5331	0	0	243	5574

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5464
X-RAY DIFFRACTION	f_angle_d	0.685	7429
X-RAY DIFFRACTION	f_dihedral_angle_d	12.817	1932
X-RAY DIFFRACTION	f_chiral_restr	0.027	860
X-RAY DIFFRACTION	f_plane_restr	0.003	954

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 (%)
2.3002-2.3679	0.3481	134	0.2864	2546	X-RAY DIFFRACTION	99
2.3679-2.4443	0.3348	135	0.2729	2568	X-RAY DIFFRACTION	99
2.4443-2.5316	0.3079	140	0.2625	2569	X-RAY DIFFRACTION	100
2.5316-2.633	0.2917	140	0.2579	2546	X-RAY DIFFRACTION	99
2.633-2.7528	0.285	152	0.2416	2558	X-RAY DIFFRACTION	99
2.7528-2.8978	0.238	162	0.2383	2558	X-RAY DIFFRACTION	100
2.8978-3.0793	0.2716	124	0.2282	2601	X-RAY DIFFRACTION	100
3.0793-3.3169	0.2648	154	0.2209	2548	X-RAY DIFFRACTION	100
3.3169-3.6505	0.1985	162	0.1926	2554	X-RAY DIFFRACTION	99
3.6505-4.1781	0.234	136	0.18	2572	X-RAY DIFFRACTION	100
4.1781-5.2617	0.1805	137	0.1528	2604	X-RAY DIFFRACTION	100
5.2617-37.5725	0.1869	153	0.1767	2612	X-RAY DIFFRACTION	100

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	4.8305	3.1302	0.5698	6.4219	0.6152	1.2648	-0.4528	0.0477	0.1218	-1.1163	0.2988	0.3085	0.2059	0.2224	0.1874	0.3938	-0.015	-0.0819	0.3118	0.0062	0.2409	-1.318	-25.1187	-31.3986
2	4.0444	0.7293	2.5358	4.4402	0.6678	4.0861	-0.0482	0.1623	0.0433	-0.7755	-0.0643	0.4235	0.1653	-0.0762	0.0084	0.3274	0.0188	0.0276	0.2201	0.0003	0.2576	-9.2888	-22.1585	-32.7281
3	1.2147	0.1396	-0.5729	3.8886	0.7946	0.4638	0.0644	-0.3147	0.0659	-0.1374	0.2278	0.908	0.0383	-0.3564	-0.3722	0.3096	-0.0556	-0.0652	0.5641	-0.0513	0.5616	-19.1395	-15.6364	-25.9334
4	3.1669	-2.6386	0.2085	2.328	-0.8752	3.245	-0.4337	-0.1603	0.0146	0.0587	0.3553	1.133	-0.1104	-0.5708	0.2006	0.3863	0.0252	-0.099	0.594	0.0196	0.7885	-23.8221	-15.2425	-31.4953
5	9.6606	1.076	1.3943	6.2863	3.7363	8.6932	-0.6108	-1.0742	0.93	-0.3651	0.0297	1.0504	-0.7464	-1.018	0.7968	0.3808	0.1068	-0.0027	0.5462	-0.1899	0.7906	-16.7633	-3.0057	-22.0521
6	3.1555	1.2025	2.3686	2.4715	0.7356	1.7512	-0.039	-0.3425	0.4497	0.275	-0.2071	0.2486	-0.1904	-0.3559	0.2869	0.4156	0.0481	0.1294	0.3833	-0.1081	0.3918	0.0806	-9.5781	-14.7098
7	1.0211	-0.0635	0.4632	6.3688	-0.3721	2.8018	0.1299	0.0008	-0.0673	0.982	-0.0963	-0.277	0.2452	-0.1211	-0.034	0.4721	-0.0261	-0.1036	0.2806	-0.0298	0.3004	11.3823	-19.4926	-7.2689
8	2.1477	2.3409	-1.4269	7.1817	-0.5741	5.2571	0.1816	-0.1127	-0.4227	0.2346	-0.1304	-0.3174	0.2075	-0.1545	-0.0281	0.3291	-0.0768	-0.0089	0.3252	-0.017	0.2234	7.7216	-23.8537	-13.9514
9	2.7259	0.9439	2.6105	5.534	1.7618	4.2709	0.2977	0.0193	-0.1812	0.3705	-0.1968	-0.7426	0.3426	0.1109	-0.1428	0.2809	-0.0426	-0.0416	0.2692	-0.0071	0.3279	11.9404	-24.2009	-16.9273
10	4.151	0.3296	2.2426	2.014	-0.5765	3.4475	-0.4551	0.7443	0.6001	-0.794	0.1339	0.4078	-0.4406	0.4253	0.3564	0.5458	-0.0703	-0.1255	0.308	0.1088	0.4593	-7.2468	-11.7175	-36.024
11	4.0903	0.4359	1.993	1.7122	0.8549	2.2735	-0.0101	-0.4355	0.3102	0.0013	-0.1122	0.1526	0.0638	-0.287	0.1054	0.3477	-0.0373	0.0523	0.2919	0.026	0.3365	0.3701	-13.602	-19.7008
12	7.9026	5.8959	2.2357	6.5657	0.8592	3.1286	0.0839	-0.1278	-0.0114	0.0326	-0.0688	0.235	0.0223	0.0277	0.0081	0.2827	-0.0036	0.0171	0.2648	-0.0282	0.2497	1.3045	-19.9709	-18.4962
13	2.134	-0.3114	1.4674	2.7822	-0.5198	2.9031	0.1744	0.1006	-0.1224	-0.6884	-0.1196	0.3868	0.0407	-0.1097	0.0571	0.6064	0.0406	-0.1326	0.3263	-0.0474	0.4026	-1.2706	23.099	-38.2805
14	2.6939	-1.4177	1.0148	3.0037	-0.3181	3.2843	0.5751	0.6045	-0.7032	-0.5934	-0.0933	0.305	0.8123	0.2742	-0.5006	1.072	0.1241	-0.144	0.61	-0.1233	0.4642	4.7857	11.1538	-49.1558
15	1.7668	-0.8417	0.8518	2.7902	-0.8861	1.6132	0.1135	0.1778	-0.2304	-0.1884	-0.1266	-0.1434	0.1231	0.0372	-0.0433	0.3337	0.0247	-0.0045	0.2592	-0.0415	0.3175	15.1043	17.6947	-22.7153
16	3.6335	-2.1406	2.5724	6.7982	-1.6639	2.3543	0.0049	-0.5228	-0.0545	0.4537	0.036	0.2262	-0.2915	-0.2355	0.0507	0.3213	0.0491	-0.0118	0.3585	0.0251	0.2585	10.0689	25.4708	-15.7583
17	2.1116	-1.0731	1.5115	1.7112	-1.0651	2.7442	0.3016	0.0421	-0.4513	-0.488	-0.0042	0.2255	0.1905	-0.1466	-0.2861	0.4945	0.0045	-0.1059	0.2592	-0.0668	0.4352	3.8881	16.3679	-31.0793

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -5 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 77 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 78 through 100 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 101 through 121 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 122 through 146 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 147 through 186 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 187 through 204 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 205 through 227 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 228 through 262 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 263 through 294 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 295 through 339 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 340 through 361 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid -4 through 100 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 101 through 146 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 147 through 227 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 228 through 262 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 263 through 361 )

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