PDB-4cph: trans-divalent streptavidin with love-hate ligand 4

ID or keywords:

Entry

Database: PDB / ID: 4cph

Title

trans-divalent streptavidin with love-hate ligand 4

Components

(STREPTAVIDIN

) x 2

Keywords

BIOTIN BINDING PROTEIN /

AVIDIN /

BIOTIN / STRAIN / BIOTINYLATED /

STERIC CLASH / STRAINED /

HINDERED /

FORCE / LIGAND SERIES / AFFINITY

Function / homology

Function and homology information

biotin binding / extracellular region
Similarity search - Function

Biological species

STREPTOMYCES AVIDINII (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 Å

Authors

Fairhead, M. / Shen, D. / Chan, L.K.M. / Lowe, E.D. / Donohoe, T.J. / Howarth, M.

Citation

Journal: Bioorg.Med.Chem. / Year: 2014
Title: Love-Hate Ligands for High Resolution Analysis of Strain in Ultra-Stable Protein/Small Molecule Interaction.
Authors: Fairhead, M. / Shen, D. / Chan, L.K.M. / Lowe, E.D. / Donohoe, T.J. / Howarth, M.

History

Deposition	Feb 6, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 6, 2014	Provider: repository / Type: Initial release
Revision 1.1	Aug 27, 2014	Group: Database references
Revision 1.2	Oct 1, 2014	Group: Database references
Revision 1.3	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4cph.cif.gz	204.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4cph.ent.gz	166.5 KB	Display	PDB format
PDBx/mmJSON format	4cph.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cp/4cph ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cph	HTTPS FTP

-
Related structure data

Related structure data	4cpeC 4cpfC 4cpiC 3ry1S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7efd-1 7efc-1 4cpi-2 1n9y-d 4y5d-d 5n99-2 6lng-1 5to2-d 6udb-d 4y59-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: STREPTAVIDIN

B: STREPTAVIDIN

C: STREPTAVIDIN

D: STREPTAVIDIN

hetero molecules

56.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	90.740, 47.490, 104.880
Angle α, β, γ (deg.)	90.00, 101.14, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	STREPTAVIDIN / Mass: 13250.320 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-163 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P22629
#2: Protein	STREPTAVIDIN / Mass: 14056.019 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P22629
#3: Chemical	ChemComp-LH4 / 5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4- d]imidazolidin-4-yl]-N'-{2,6-bis[4-(morpholine-4- sulfonyl)phenyl]phenyl}pentanehydrazide Mass: 784.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₆H₄₄N₆O₈S₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	5-[(3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4- D]IMIDAZOLIDIN-4-YL]-N'-{2,6-BIS[4-(MORPHOLINE-4- ...5-[(3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4- D]IMIDAZOLIDIN-4-YL]-N'-{2,6-BIS[4-(MORPHOLINE-4- SULFONYL)PHENYL]PHENYL}PENTANEHYDRAZIDE (LH4): LOVE-HATE LIGAND 4 LH4

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54 % / Description: NONE
Crystal grow	Method: vapor diffusion, sitting drop / pH: 4.5 Details: 75% AMMONIUM SULPHATE, 25% SODIUM ACETATE PH4.5. SITTING DROP

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
Detector	Type: DECTRIS PIXEL / Detector: PIXEL / Date: May 28, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.64→41.9 Å / Num. obs: 52123 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / B_iso Wilson estimate: 18.96 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 8.4
Reflection shell	Resolution: 1.64→1.7 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 95.5

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
xia2		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RY1

3ry1

Resolution: 1.64→41.902 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 25.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.232	2661	5.1 %
R_work	0.2009	-	-
obs	0.2025	52101	96.52 %

Solvent computation

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

Displacement parameters

B_iso mean: 28.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.64→41.902 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3563	0	106	254	3923

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3935
X-RAY DIFFRACTION	f_angle_d	1.229	5428
X-RAY DIFFRACTION	f_dihedral_angle_d	12.913	1344
X-RAY DIFFRACTION	f_chiral_restr	0.051	597
X-RAY DIFFRACTION	f_plane_restr	0.005	728

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 (%)
1.64-1.6698	0.283	136	0.2693	2522	X-RAY DIFFRACTION	95
1.6698-1.7019	0.3116	149	0.2614	2585	X-RAY DIFFRACTION	96
1.7019-1.7367	0.3056	124	0.2524	2500	X-RAY DIFFRACTION	96
1.7367-1.7744	0.289	146	0.246	2613	X-RAY DIFFRACTION	96
1.7744-1.8157	0.2736	145	0.2273	2553	X-RAY DIFFRACTION	96
1.8157-1.8611	0.2304	134	0.2151	2536	X-RAY DIFFRACTION	96
1.8611-1.9115	0.2599	146	0.2097	2600	X-RAY DIFFRACTION	96
1.9115-1.9677	0.2421	160	0.2057	2576	X-RAY DIFFRACTION	96
1.9677-2.0312	0.2294	129	0.1957	2560	X-RAY DIFFRACTION	96
2.0312-2.1038	0.2286	133	0.1945	2590	X-RAY DIFFRACTION	96
2.1038-2.188	0.2244	154	0.1876	2583	X-RAY DIFFRACTION	97
2.188-2.2876	0.2047	140	0.1845	2595	X-RAY DIFFRACTION	97
2.2876-2.4082	0.2248	130	0.2002	2654	X-RAY DIFFRACTION	97
2.4082-2.5591	0.2238	140	0.2057	2642	X-RAY DIFFRACTION	97
2.5591-2.7566	0.2328	147	0.2104	2599	X-RAY DIFFRACTION	98
2.7566-3.034	0.2508	139	0.2029	2677	X-RAY DIFFRACTION	98
3.034-3.4728	0.2208	141	0.192	2638	X-RAY DIFFRACTION	98
3.4728-4.3746	0.2276	130	0.178	2684	X-RAY DIFFRACTION	97
4.3746-41.9152	0.2089	138	0.2029	2733	X-RAY DIFFRACTION	97

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	2.205	1.0919	-0.4454	2.8485	-0.3597	1.953	-0.1052	-0.2286	0.2111	0.0988	0.0134	-0.0452	-0.041	0.3486	0.0343	0.1642	0.049	-0.0392	0.2912	0.0154	0.2831	99.9664	-8.5235	148.1851
2	2.2014	-0.7556	-1.1926	2.7042	1.4171	2.5833	0.0366	-0.1256	0.0382	0.3066	0.0742	-0.4027	0.122	0.2779	-0.117	0.1812	0.0309	-0.0345	0.1947	0.0266	0.196	94.6847	-8.9284	147.1209
3	1.1188	-0.3922	-0.5056	1.9982	0.7571	2.2665	0.0511	-0.1352	0.151	0.1279	-0.0158	-0.1051	-0.0603	0.0086	-0.1044	0.1599	0.0051	0.0121	0.1726	-0.0003	0.167	90.9129	-0.1699	146.1294
4	2.2708	-0.0832	-0.2609	2.3769	-0.113	2.366	0.0989	0.0164	-0.0824	-0.0822	0.0051	-0.068	-0.0657	0.1958	0.0657	0.0825	0.0043	0.0006	0.1187	-0.003	0.1186	94.5913	-1.2194	137.6009
5	3.4067	-1.4784	-1.4032	3.528	0.0608	2.8906	0.0182	0.0072	0.0557	-0.1018	0.0591	0.4605	0.0107	-0.344	-0.1131	0.2513	-0.0047	-0.0355	0.2872	0.0095	0.2257	79.8943	3.805	110.3063
6	3.757	-1.0784	-0.3401	5.5914	-1.0878	2.6634	0.2412	0.1256	0.3003	-0.0643	-0.3429	0.7182	-0.6267	-0.9568	-0.0033	0.1761	0.0694	-0.0317	0.29	-0.0429	0.2609	82.7653	10.4159	111.9697
7	1.8433	0.1466	-0.156	3.493	0.4826	2.1878	0.0205	0.1865	-0.0433	-0.5933	0.0285	0.3346	-0.0544	-0.1668	-0.0447	0.2228	0.0065	-0.0415	0.2131	0.0132	0.1862	85.8062	0.3397	109.9581
8	1.4116	0.3662	0.1868	2.1441	0.7433	1.6192	0.0571	0.029	0.1076	-0.1356	-0.0442	0.222	-0.3066	-0.1112	-0.014	0.2067	0.0148	-0.0104	0.1481	0.0114	0.1438	88.0316	7.7207	116.8191
9	3.0563	0.0299	0.8667	3.3688	0.9054	3.6494	0.0605	0.1673	-0.0523	-0.0467	-0.0665	0.5288	0.1542	-0.4593	0.0191	0.168	-0.0165	0.0095	0.22	0.0087	0.2053	81.4873	-0.761	119.2154
10	1.2231	0.8826	0.2216	2.0595	0.1987	2.444	0.0664	-0.2199	0.22	0.1323	-0.0758	0.1057	-0.1768	-0.2094	0.0209	0.1685	0.0198	0.0217	0.1576	0.0042	0.1865	87.1927	5.8861	126.0586
11	1.6649	-1.0624	0.0944	3.3882	-0.9704	1.9413	0.0243	0.2328	-0.1473	0.014	-0.0368	-0.1747	-0.1034	0.3085	0.017	0.207	-0.0466	-0.0282	0.3117	-0.0013	0.3251	106.4983	2.5856	114.7331
12	1.2779	0.4211	0.7486	3.6438	1.704	4.1297	0.0534	0.0211	0.035	-0.2232	0.1327	-0.4512	-0.0435	0.3864	-0.1389	0.1921	-0.0207	0.0267	0.2034	0.0069	0.1932	101.2849	3.0495	113.9876
13	1.3667	-0.0835	-0.2284	2.4435	1.5025	2.4785	0.0497	0.083	-0.1362	-0.1638	-0.0117	-0.099	0.0881	0.0968	-0.0794	0.2213	-0.0096	0.0036	0.1791	0.0076	0.148	97.3284	-5.2551	113.7988
14	4.4523	1.8584	0.1086	4.595	0.1571	2.3772	0.1747	-0.2278	0.0759	0.1524	-0.1505	0.0409	0.0981	-0.0192	-0.0118	0.1554	0.0186	-0.0132	0.1263	0.0109	0.0896	93.6798	-5.3572	122.5248
15	1.9174	1.3736	-0.5434	1.4068	-0.2081	1.7988	0.0265	0.0558	-0.2223	-0.0195	0.0578	-0.3971	0.1002	0.4094	0.0021	0.1253	0.0115	-0.0246	0.2667	-0.0065	0.2405	104.1809	-3.1518	123.537
16	2.2431	0.7717	0.8579	2.4328	0.3415	3.8447	0.0158	0.2177	-0.1096	-0.165	0.0175	0.2591	0.1724	-0.2779	-0.0199	0.2064	0.0075	0.0119	0.2983	-0.0061	0.2704	73.5687	-9.8501	142.2596
17	2.1079	-0.69	0.0375	3.5759	-0.1362	2.4855	0.0527	0.0231	-0.0688	-0.0522	0.0173	0.4186	0.0471	-0.272	-0.0079	0.106	-0.0138	0.0053	0.1976	0.0107	0.1857	79.1222	-9.0046	143.7475
18	2.3695	-0.2305	-0.2143	2.1057	0.1925	1.8992	0.0365	0.0772	-0.1369	-0.0101	-0.166	0.1091	0.3027	-0.1522	0.1007	0.1345	-0.0078	0.0048	0.128	0.0026	0.1316	83.9443	-15.3178	138.6159
19	2.7399	0.1956	-0.2877	1.7319	0.1302	2.1565	0.2122	-0.1085	0.2237	-0.119	-0.1003	0.3225	-0.1779	-0.2947	-0.0766	0.1499	0.0436	-0.008	0.2056	-0.0059	0.2337	78.5194	-4.8632	134.983
20	3.3705	-0.9057	-1.2714	1.8671	0.2188	2.3673	-0.0941	0.1806	-0.1282	-0.1298	0.0388	0.0323	0.2242	-0.0594	0.089	0.1745	0.003	-0.0188	0.153	0.0018	0.1643	86.6039	-11.3561	130.8107

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 16 THROUGH 37 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 38 THROUGH 78 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 79 THROUGH 97 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 98 THROUGH 135 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 16 THROUGH 37 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 38 THROUGH 49 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 50 THROUGH 70 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 71 THROUGH 97 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 98 THROUGH 112 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 113 THROUGH 135 )
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESID 16 THROUGH 37 )
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESID 38 THROUGH 78 )
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESID 79 THROUGH 97 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 98 THROUGH 122 )
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESID 123 THROUGH 135 )
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESID 16 THROUGH 37 )
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESID 38 THROUGH 78 )
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESID 79 THROUGH 97 )
19	X-RAY DIFFRACTION	19	CHAIN D AND (RESID 98 THROUGH 112 )
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESID 113 THROUGH 134 )

-
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://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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi