PDB-5aq9: DARPin-based Crystallization Chaperones exploit Molecular Geometr...

ID or keywords:

Entry

Database: PDB / ID: 5aq9

Title

DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography

Components

MALTOSE-BINDING PERIPLASMIC PROTEIN
OFF7_DB08V4

Keywords

CHAPERONE / CRYSTALLIZATION CHAPERONE / DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) / RIGID DOMAIN FUSION

Function / homology

Function and homology information

detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...
Similarity search - Function

Biological species

SYNTHETIC CONSTRUCT (others)

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.86 Å

Authors

Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A.

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Darpin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
Authors: Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A.

History

Deposition	Sep 21, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 6, 2016	Group: Database references
Revision 1.2	May 18, 2016	Group: Database references
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5aq9.cif.gz	880.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5aq9.ent.gz	751.3 KB	Display	PDB format
PDBx/mmJSON format	5aq9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5aq9_validation.pdf.gz	446.7 KB	Display	wwPDB validaton report
Full document	5aq9_full_validation.pdf.gz	452.4 KB	Display
Data in XML	5aq9_validation.xml.gz	61.9 KB	Display
Data in CIF	5aq9_validation.cif.gz	91.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aq/5aq9 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/5aq9	HTTPS FTP

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Related structure data

Related structure data	5aq7C 5aq8C 5aqaC 5aqbC 1svxS 3dtmS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3let-2 3zik-2 4guj-d 1f5s-d 4cno-1 6h5c-d 4cnn-d 3o1n-d 3hjc-d 3cnx-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) 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

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (6) #221 - May 2018 Human Papillomavirus and Vaccines similarity (6) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (6)

Deposited unit

A: OFF7_DB08V4

B: MALTOSE-BINDING PERIPLASMIC PROTEIN

C: OFF7_DB08V4

D: MALTOSE-BINDING PERIPLASMIC PROTEIN

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

1

A: OFF7_DB08V4

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

2

C: OFF7_DB08V4

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

3

B: MALTOSE-BINDING PERIPLASMIC PROTEIN

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

4

D: MALTOSE-BINDING PERIPLASMIC PROTEIN

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

Unit cell

Length a, b, c (Å)	41.480, 191.120, 219.510
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	OFF7_DB08V4 Mass: 45678.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE
#2: Protein	MALTOSE-BINDING PERIPLASMIC PROTEIN / MBP / MMBP / MALTODEXTRIN-BINDING PROTEIN Mass: 43172.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE / References: UniProt: P0AEX9
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1059 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48 % / Description: NONE
Crystal grow	pH: 7.1 Details: PEG6000 17% W/V, AMMONIUM CHLORIDE 0.2 M, HEPES 0.05 M, PH 7.1

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2012 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR
Radiation	Monochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.86→47.78 Å / Num. obs: 148199 / % possible obs: 1 % / Observed criterion σ(I): 1.96 / Redundancy: 13.1 % / B_iso Wilson estimate: 29.69 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 21.83
Reflection shell	Resolution: 1.86→1.93 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1.81 / % possible all: 1

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3DTM AND 1SVX CHAINS A AND B

3dtm

1svx

Resolution: 1.86→48.047 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 19.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2038	7409	5 %
R_work	0.1816	-	-
obs	0.1827	148181	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 47.97 Å²

Refinement step

Cycle: LAST / Resolution: 1.86→48.047 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12090	0	0	1059	13149

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12399
X-RAY DIFFRACTION	f_angle_d	0.565	16855
X-RAY DIFFRACTION	f_dihedral_angle_d	11.641	7415
X-RAY DIFFRACTION	f_chiral_restr	0.04	1878
X-RAY DIFFRACTION	f_plane_restr	0.003	2209

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 (%)
1.86-1.8811	0.2948	245	0.2808	4660	X-RAY DIFFRACTION	100
1.8811-1.9032	0.2784	241	0.2708	4576	X-RAY DIFFRACTION	100
1.9032-1.9264	0.2945	242	0.264	4593	X-RAY DIFFRACTION	100
1.9264-1.9508	0.2871	244	0.251	4641	X-RAY DIFFRACTION	100
1.9508-1.9765	0.275	248	0.2375	4711	X-RAY DIFFRACTION	100
1.9765-2.0036	0.2616	240	0.2365	4555	X-RAY DIFFRACTION	100
2.0036-2.0322	0.2499	242	0.2257	4610	X-RAY DIFFRACTION	100
2.0322-2.0625	0.233	247	0.2174	4681	X-RAY DIFFRACTION	100
2.0625-2.0948	0.2306	244	0.2168	4632	X-RAY DIFFRACTION	100
2.0948-2.1291	0.2331	244	0.2022	4636	X-RAY DIFFRACTION	100
2.1291-2.1658	0.2199	246	0.198	4671	X-RAY DIFFRACTION	100
2.1658-2.2052	0.223	243	0.1913	4626	X-RAY DIFFRACTION	100
2.2052-2.2476	0.201	243	0.1866	4626	X-RAY DIFFRACTION	100
2.2476-2.2935	0.2108	248	0.1874	4713	X-RAY DIFFRACTION	100
2.2935-2.3434	0.2061	244	0.1782	4619	X-RAY DIFFRACTION	100
2.3434-2.3979	0.188	245	0.18	4668	X-RAY DIFFRACTION	100
2.3979-2.4578	0.2054	248	0.1823	4698	X-RAY DIFFRACTION	100
2.4578-2.5243	0.2122	242	0.1744	4608	X-RAY DIFFRACTION	100
2.5243-2.5986	0.2155	251	0.177	4760	X-RAY DIFFRACTION	100
2.5986-2.6824	0.21	243	0.1762	4627	X-RAY DIFFRACTION	100
2.6824-2.7783	0.2123	250	0.176	4751	X-RAY DIFFRACTION	100
2.7783-2.8895	0.2068	244	0.1835	4629	X-RAY DIFFRACTION	100
2.8895-3.021	0.2187	249	0.1836	4729	X-RAY DIFFRACTION	100
3.021-3.1802	0.2188	249	0.1931	4741	X-RAY DIFFRACTION	100
3.1802-3.3794	0.1898	247	0.1826	4696	X-RAY DIFFRACTION	100
3.3794-3.6403	0.2091	250	0.1722	4741	X-RAY DIFFRACTION	100
3.6403-4.0065	0.1741	251	0.1626	4779	X-RAY DIFFRACTION	100
4.0065-4.5858	0.1626	255	0.1437	4842	X-RAY DIFFRACTION	100
4.5858-5.7761	0.171	255	0.1618	4839	X-RAY DIFFRACTION	100
5.7761-48.0632	0.2042	269	0.1857	5114	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	2.2387	1.1731	-0.4358	2.359	0.8863	3.0792	0.3849	-0.5359	-0.5345	-0.0694	-0.0123	0.0029	0.9183	-0.039	-0.1761	0.8754	0.0978	-0.2361	0.6435	0.1822	1.0042	-31.7616	-15.4525	-9.0971
2	2.3591	0.2103	0.7311	1.3869	0.4981	1.8485	0.4485	-0.0196	-0.4883	0.1079	0.0361	-0.2759	-0.0004	-0.0128	-0.3746	0.5144	-0.0076	-0.0277	0.3202	0.0928	0.543	-20.7255	-4.1467	-4.672
3	1.4712	0.7038	-0.2195	1.8214	0.212	1.0544	0.0024	-0.165	-0.1648	0.1205	-0.0557	-0.0974	0.0871	0.0836	0.0465	0.1159	0.0137	0.0007	0.2388	-0.0312	0.1845	-1.2051	30.9074	-4.8906
4	2.0725	-0.6753	-0.0925	1.2305	0.3035	1.4346	-0.1243	0.025	-0.8084	-0.0938	-0.0908	0.0436	0.4691	-0.0394	0.1331	1.3127	-0.0775	-0.3778	0.5699	0.1124	0.9793	-4.9546	-56.4613	21.7427
5	1.0633	-0.3145	-0.0679	1.0058	-0.3767	0.3736	0.0689	-0.1558	-0.09	-0.0042	0.0903	-0.026	0.2111	0.1193	-0.1187	0.9643	-0.0372	-0.3414	0.4041	0.0513	0.5533	-6.0561	-30.9742	14.4604
6	0.9741	0.1585	0.1315	0.8861	-0.3747	0.6066	0.1357	-0.0291	-0.2945	-0.1157	0.0554	0.1394	0.2567	0.1198	-0.1992	0.98	-0.0475	-0.3009	0.4908	0.1088	0.5669	-7.3396	-33.544	17.3499
7	2.6387	1.3221	-0.6364	2.0683	0.6638	2.3105	-0.3093	-0.1528	0.2616	-0.4812	-0.163	-0.5577	-0.1465	0.0973	0.1806	0.6353	-0.0231	0.1881	0.626	-0.0415	0.4552	27.3555	40.8419	-56.337
8	1.4196	0.766	-0.594	1.236	-0.7716	1.244	-0.1116	0.1531	-0.1437	-0.2401	-0.0247	-0.1256	0.1322	0.0497	0.0889	0.4412	-0.0479	0.1145	0.3973	-0.035	0.2925	16.5901	32.5825	-47.3487
9	1.5007	0.1831	-0.0433	2.0656	0.3749	1.6196	0.0198	0.0921	-0.3216	0.1057	-0.0569	0.074	0.0496	-0.0091	0.0248	0.1687	-0.0037	0.0336	0.3086	-0.0826	0.358	-4.077	1.7299	-33.2226
10	1.9135	-0.0318	0.0921	1.0046	0.397	2.0242	0.0411	0.2863	0.6004	0.8192	-0.1064	-0.156	-0.3102	0.189	0.0446	0.8351	-0.0014	0.0222	0.4146	0.1526	0.6503	0.6144	90.6594	-44.7105
11	1.2313	-0.3277	0.0468	1.8673	-0.0654	0.5515	-0.075	0.0657	0.1987	0.3701	0.0888	0.0623	-0.2661	-0.0569	-0.0052	0.7383	-0.0396	0.1521	0.3668	0.0657	0.3162	1.912	65.4164	-41.839

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 23 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 24 THROUGH 158 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 159 THROUGH 422 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 18 THROUGH 87 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 88 THROUGH 297 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 298 THROUGH 388 )
7	X-RAY DIFFRACTION	7	CHAIN 'C' AND (RESID 4 THROUGH 24 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 25 THROUGH 158 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 159 THROUGH 422 )
10	X-RAY DIFFRACTION	10	CHAIN 'D' AND (RESID 18 THROUGH 97 )
11	X-RAY DIFFRACTION	11	CHAIN 'D' AND (RESID 98 THROUGH 388 )

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