PDB-6wpn: Crystal structure of a putative oligosaccharide periplasmic-bindi...

ID or keywords:

Entry

Database: PDB / ID: 6wpn

Title

Crystal structure of a putative oligosaccharide periplasmic-binding protein from Synechococcus sp. MITs9220

Components

Substrate-binding protein

Keywords

TRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / sugar-binding protein

Biological species

Synechococcus sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

Ford, B.A. / Michie, K.A. / Paulsen, I.T. / Mabbutt, B.C. / Shah, B.S.

Funding support

Australia, 2items

Citation

Journal: Sci Rep / Year: 2022
Title: Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220.
Authors: Ford, B.A. / Michie, K.A. / Paulsen, I.T. / Mabbutt, B.C. / Shah, B.S.

History

Deposition	Apr 27, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 12, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2022	Group: Database references / Category: citation / citation_author / database_2 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 / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wpn.cif.gz	362.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6wpn.ent.gz	263.4 KB	Display	PDB format
PDBx/mmJSON format	6wpn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wpn_validation.pdf.gz	458.1 KB	Display	wwPDB validaton report
Full document	6wpn_full_validation.pdf.gz	464.6 KB	Display
Data in XML	6wpn_validation.xml.gz	28.3 KB	Display
Data in CIF	6wpn_validation.cif.gz	38.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/6wpn ftp://data.pdbj.org/pub/pdb/validation_reports/wp/6wpn	HTTPS FTP

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Related structure data

Related structure data	6wpmSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6wpm-d 7c6y-d 4pfa-2 1qzd-d 4mrq-d 6s2t-d 7c6j-1 4g22-2 6zj4-d 7c6x-6 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Substrate-binding protein

B: Substrate-binding protein

hetero molecules

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

1

A: Substrate-binding protein

hetero molecules

defined by author
Evidence: gel filtration, Gel filtration shows monomeric size
47.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Substrate-binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.947, 69.525, 83.721
Angle α, β, γ (deg.)	90.000, 94.702, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#1: Protein	Substrate-binding protein Mass: 47341.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: MITs9220 / Gene: 00121 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H₂O
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 Å³/Da / Density % sol: 33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Ammonium sulphate (2 M), Tris (0.1 M, pH 8.5)

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX2 / Wavelength: 0.9537 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 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: 2.29→46.79 Å / Num. obs: 30536 / % possible obs: 99.5 % / Redundancy: 3.8 % / B_iso Wilson estimate: 48.08 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.042 / R_rim(I) all: 0.083 / Net I/σ(I): 10.5

Reflection shell

Resolution (Å)	Redundancy (%)	Num. unique obs	CC_1/2	Diffraction-ID	% possible all
2.38-2.38	3.6	2892	0.534	1	96.5
8.9-46.79	3.6	549	0.999	1	98

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Processing

Software

Name	Version	Classification
REFMAC	5	refinement
PHENIX	1.15.2_3472	refinement
PDB_EXTRACT	3.22	data extraction
Aimless		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6WPM

6wpm

Resolution: 2.29→41.72 Å / SU ML: 0.3553 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.5977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2471	1917	6.42 %	RANDOM
R_work	0.2012	27950	-	-
obs	0.2042	29867	96.2 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 65.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.29→41.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6107	0	20	38	6165

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0041	6270
X-RAY DIFFRACTION	f_angle_d	0.6816	8547
X-RAY DIFFRACTION	f_chiral_restr	0.0443	977
X-RAY DIFFRACTION	f_plane_restr	0.0051	1123
X-RAY DIFFRACTION	f_dihedral_angle_d	16.1026	2316

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 (%)
2.29-2.35	0.4219	120	0.3603	1592	X-RAY DIFFRACTION	77.96
2.35-2.41	0.4085	133	0.3101	1922	X-RAY DIFFRACTION	91.74
2.41-2.48	0.3174	126	0.2915	1941	X-RAY DIFFRACTION	94.04
2.48-2.56	0.3307	127	0.265	1929	X-RAY DIFFRACTION	94.75
2.56-2.65	0.3476	137	0.2565	1990	X-RAY DIFFRACTION	96.16
2.65-2.76	0.2905	149	0.2602	1995	X-RAY DIFFRACTION	97.28
2.76-2.89	0.3221	124	0.2391	2061	X-RAY DIFFRACTION	98.03
2.89-3.04	0.2665	149	0.2336	2015	X-RAY DIFFRACTION	98.72
3.04-3.23	0.3422	139	0.2276	2044	X-RAY DIFFRACTION	99.41
3.23-3.48	0.2515	137	0.2139	2081	X-RAY DIFFRACTION	99.73
3.48-3.83	0.2333	147	0.1882	2074	X-RAY DIFFRACTION	99.91
3.83-4.38	0.2027	140	0.1611	2092	X-RAY DIFFRACTION	99.82
4.38-5.52	0.1849	141	0.1625	2091	X-RAY DIFFRACTION	99.87
5.52-41.72	0.212	148	0.1759	2123	X-RAY DIFFRACTION	99.13

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	4.37683220582	-0.950601727686	1.24559435939	3.77168784107	-0.280534484414	5.91959316822	0.0616211127959	-0.219043080497	0.365965819084	-0.477842962522	0.0828407796701	0.149200079776	-0.324514957219	0.414859938032	-0.0980556767326	0.659103721416	-0.148999642815	0.0608390806691	0.576872757236	-0.143544434619	0.569617311571	-5.75546948903	32.3994050559	9.13242416327
2	7.45894944262	1.33163980569	-3.18101718109	1.62037753502	-0.473152040275	1.78144615955	-0.0176385722802	-0.137632144067	-0.550154529657	0.217183061114	-0.165436516082	0.222670691194	0.358424438557	-0.0596489274255	0.209512230084	0.787016993984	-0.130734383664	0.021854316682	0.434455077717	-0.0691561127477	0.358616349541	5.50674689547	17.9465738094	1.15293134088
3	4.47872593442	2.11070151054	-2.0687267363	5.73610375325	-1.51781970212	6.72843128473	-0.0997324381297	-0.340025638823	-0.358307179714	0.130499469639	0.0249698690379	0.0805874544946	0.676805932312	0.364975553981	0.0831777627583	0.366367295645	0.0901472269888	-0.0417294686672	0.338409627912	-0.00317478068075	0.287683887748	26.4363548061	17.4623042835	7.39122112961
4	3.11752193033	-0.0517026731328	-0.0633450725824	0.622626631191	0.505626390395	1.13724559765	-0.0964121571937	-0.110450798231	-0.164508123626	0.0397402679352	0.084827454145	0.116449729004	0.23087322281	-0.209416289351	0.0121424707991	0.529841107592	-0.0183157807197	0.00623419834642	0.310967607497	-0.0181134749654	0.295060498573	11.0915712572	22.66956644	1.44072004053
5	5.41796097643	0.313116684596	2.1985479368	4.55090542516	-1.79450594675	8.78652103529	0.111010498035	0.563125961142	-0.738395341147	-0.220322198557	-0.267801444122	-0.302491523675	1.12684540673	0.310634733024	0.114962707298	0.610614864139	0.00235320166006	0.0159630241267	0.694877427344	-0.0204791377504	0.422355167876	-0.395565921861	24.1734769045	38.9475373773
6	7.552627753	-1.96999415314	7.59303662614	2.82620922881	-2.28484693017	7.6940658752	-0.616352562233	0.304402499946	1.53058608027	-0.489365032463	0.0359446873793	0.301279445815	-0.708620905479	-0.0334228325761	0.596875418698	0.645274354106	-0.0179304475608	-0.130881977228	0.638417159944	0.0869300262535	0.474873236639	0.657553625199	42.2079681821	41.6411284241
7	1.50916508439	-0.0991293488878	-2.50057817788	1.8066556665	-0.0211555413741	3.95865458478	-0.340079121553	-0.787073202426	0.703463875383	0.572856652972	0.367368328158	-0.882746428774	-0.712717693858	0.260698294182	-0.0694430553432	0.677321592422	0.171552212131	-0.21658166573	0.883150757939	0.0181744735864	0.225782898608	32.6768950829	39.6389028079	36.5981005569
8	2.90131403846	-1.6239485316	0.639292125899	3.51884758785	-1.69107737167	5.1771442254	-0.132709984696	-0.514112043838	-0.252353217838	0.436691287345	0.225802392387	0.0522416859354	-0.172061595453	0.419513412826	-0.130453863233	0.429763185117	-0.00930332483514	0.0184173166384	0.497755666932	0.0554827391956	0.297869603425	26.8528790514	36.9079125864	28.5370706231
9	2.07172494974	6.22349674441	0.372006698898	5.29860866393	0.79828532332	1.07416509394	-0.984425925943	-0.684341248769	-0.673650169508	-0.276338323896	0.479574651753	-0.000957769150921	-0.0250237319409	0.251996085995	0.297215199244	0.546035529038	0.0197341933662	-0.0925905307667	0.905488501307	-0.0492784852131	0.323485897481	6.63082295337	35.6295399358	37.281350579
10	6.85955148717	-0.39475944449	1.97072877342	0.786919971537	-0.0284974412973	3.42454226146	0.0558589364519	-0.56971560048	-0.347467379915	0.166758298243	-0.0335656103854	-0.160904875312	0.363821164436	0.770431463377	-0.0492825478654	0.618761668258	0.0544290456941	0.0248469853725	0.830583391532	0.125831481818	0.368111039828	14.603706859	32.2283745489	51.9151640175
11	2.24201905541	0.254847202071	0.411126668271	1.46757989519	-0.19612371772	7.99337353532	0.222809336375	-0.145474071543	-0.111379852891	0.509755219873	0.150074933283	0.228213083222	-0.235510658987	-0.367890721072	-0.380842327339	0.525506439614	-0.0208661437277	0.034725028722	0.263742415887	0.0699805626521	0.355562142291	18.3580950921	40.8805745777	22.4318372482
12	1.7399360978	3.54181689084	-1.32491851098	7.923011836	-1.11581931814	5.47209111183	-0.0733730517457	1.48946478235	0.745492861523	-0.510794015373	0.607003568924	0.755094171928	-0.274141704658	-1.18887585948	-0.396211691946	0.460447658678	0.0575472138642	-0.0407514546946	0.582366811156	0.101152530225	0.355237461112	11.0680995174	45.4361785392	13.3841642292

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 72 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 73 through 145 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 146 through 226 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 227 through 410 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 10 through 90 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 91 through 118 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 119 through 159 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 160 through 266 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 267 through 291 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 292 through 356 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 357 through 389 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 390 through 410 )

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