PDB-8kd0: Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubi...

ID or keywords:

Entry

Database: PDB / ID: 8kd0

Title

Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose

Components

Probable binding protein component of ABC sugar transporter

Keywords

TRANSPORT PROTEIN / ABC transporter / glucose transporter / periplasmic binding protein / solute-binding protein

Function / homology

carbohydrate transport / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / beta-D-galactopyranose / Probable binding protein component of ABC sugar transporter

Function and homology information

Biological species

Candidatus Pelagibacter ubique HTCC1062 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.675 Å

Authors

Clifton, B.E. / Laurino, P.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose
Authors: Clifton, B.E. / Alcolombri, U. / Jackson, C.J. / Laurino, P.

History

Deposition	Aug 8, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8kd0.cif.gz	212.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8kd0.ent.gz	129 KB	Display	PDB format
PDBx/mmJSON format	8kd0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8kd0_validation.pdf.gz	794.8 KB	Display	wwPDB validaton report
Full document	8kd0_full_validation.pdf.gz	795.2 KB	Display
Data in XML	8kd0_validation.xml.gz	15.9 KB	Display
Data in CIF	8kd0_validation.cif.gz	22.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kd/8kd0 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/8kd0	HTTPS FTP

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Related structure data

Related structure data	8hqqS 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	#208 - Apr 2017 Glucose Transporters similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (2) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (2)

Deposited unit

A: Probable binding protein component of ABC sugar transporter

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	43.879, 43.879, 328.555
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein

Probable binding protein component of ABC sugar transporter

Mass: 44926.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Candidatus Pelagibacter ubique HTCC1062 (bacteria)
Strain: HTCC1062 / Gene: SAR11_0769 / Plasmid: pET-28a(+) / Production host:

Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express / References: UniProt: Q4FMK2

#2: Sugar

ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H₂O

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: 2.14 Å³/Da / Density % sol: 42.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 20% (v/v) 2-propanol, 0.1 M MES pH 6.5, 23% (w/v) PEG 1500. 1.2 uL protein + 1.2 uL precipitant.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.67→46.936 Å / Num. obs: 43960 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.135 / R_rim(I) all: 0.141 / Net I/σ(I): 11.08
Reflection shell	Resolution: 1.67→1.78 Å / Redundancy: 11.37 % / R_merge(I) obs: 1.608 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 6771 / CC_1/2: 0.864 / R_rim(I) all: 1.683 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
XDS	Jun 30, 2023	data reduction
XDS	Jun 30, 2023	data scaling
MOLREP	11.9.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8HQQ

8hqq

Resolution: 1.675→38.029 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.952 / WR_factor R_free: 0.23 / WR_factor R_work: 0.197 / SU B: 7.858 / SU ML: 0.106 / Average fsc free: 0.9499 / Average fsc work: 0.9563 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2288	2217	5.044 %
R_work	0.1937	41733	-
all	0.195	-	-
obs	-	43950	99.547 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 40.44 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.066 Å²	0.533 Å²	-0 Å²
2-	-	1.066 Å²	0 Å²
3-	-	-	-3.457 Å²

Refinement step

Cycle: LAST / Resolution: 1.675→38.029 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2933	0	12	81	3026

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	3035
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2791
X-RAY DIFFRACTION	r_angle_refined_deg	1.368	1.628	4128
X-RAY DIFFRACTION	r_angle_other_deg	0.484	1.573	6421
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.252	5	404
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.328	5	7
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.653	10	466
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.733	10	128
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	448
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3611
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	682
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	649
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	2476
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1548
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1596
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	104
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.208	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.139	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.159	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.864	2.62	1595
X-RAY DIFFRACTION	r_mcbond_other	1.857	2.62	1595
X-RAY DIFFRACTION	r_mcangle_it	2.368	4.699	1994
X-RAY DIFFRACTION	r_mcangle_other	2.368	4.7	1995
X-RAY DIFFRACTION	r_scbond_it	2.664	2.85	1440
X-RAY DIFFRACTION	r_scbond_other	2.663	2.849	1441
X-RAY DIFFRACTION	r_scangle_it	3.909	5.126	2130
X-RAY DIFFRACTION	r_scangle_other	3.908	5.125	2131
X-RAY DIFFRACTION	r_lrange_it	4.404	24.964	3471
X-RAY DIFFRACTION	r_lrange_other	4.401	24.927	3462

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.675-1.718	0.355	142	0.329	2836	0.331	3165	0.873	0.886	94.0916	0.322
1.718-1.765	0.311	163	0.319	2975	0.318	3138	0.894	0.893	100	0.306
1.765-1.816	0.29	163	0.294	2877	0.294	3041	0.934	0.921	99.9671	0.276
1.816-1.872	0.284	97	0.25	2807	0.251	2905	0.939	0.949	99.9656	0.228
1.872-1.933	0.235	147	0.247	2718	0.246	2867	0.958	0.952	99.9302	0.221
1.933-2.001	0.244	173	0.218	2650	0.22	2825	0.953	0.963	99.9292	0.189
2.001-2.076	0.27	126	0.209	2489	0.211	2616	0.954	0.969	99.9618	0.182
2.076-2.161	0.207	131	0.186	2437	0.187	2568	0.972	0.976	100	0.163
2.161-2.257	0.254	139	0.2	2329	0.203	2470	0.957	0.973	99.919	0.178
2.257-2.366	0.229	140	0.192	2271	0.194	2411	0.969	0.977	100	0.173
2.366-2.494	0.223	109	0.185	2133	0.187	2242	0.967	0.978	100	0.171
2.494-2.644	0.21	100	0.176	2084	0.178	2184	0.964	0.981	100	0.164
2.644-2.826	0.237	84	0.194	1966	0.196	2050	0.963	0.976	100	0.189
2.826-3.051	0.236	117	0.206	1795	0.208	1912	0.965	0.973	100	0.205
3.051-3.34	0.262	89	0.215	1681	0.217	1770	0.961	0.971	100	0.217
3.34-3.731	0.222	86	0.192	1533	0.194	1619	0.976	0.979	100	0.205
3.731-4.301	0.194	72	0.158	1389	0.159	1461	0.974	0.985	100	0.178
4.301-5.251	0.17	48	0.146	1193	0.147	1243	0.984	0.987	99.8391	0.174
5.251-7.356	0.252	54	0.186	967	0.189	1021	0.973	0.982	100	0.227
7.356-38.029	0.195	37	0.188	603	0.188	640	0.974	0.979	100	0.255

Refinement TLS params.

Method: refined / Origin x: 0.229 Å / Origin y: 8.0484 Å / Origin z: 28.2114 Å

	11	12	13	21	22	23	31	32	33
T	0.0342 Å²	-0.0061 Å²	0.0121 Å²	-	0.0236 Å²	0.0067 Å²	-	-	0.0542 Å²
L	0.9646 °²	-0.0956 °²	-0.1493 °²	-	0.6417 °²	0.3177 °²	-	-	5.5189 °²
S	-0.0269 Å °	-0.1086 Å °	0.005 Å °	0.1386 Å °	-0.0348 Å °	0.0371 Å °	0.1188 Å °	-0.1703 Å °	0.0617 Å °

Refinement TLS group

Selection: ALL

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