PDB-4wwh: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (I...

ID or keywords:

Entry

Database: PDB / ID: 4wwh

Title

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM MYCOBACTERIUM SMEGMATIS (MSMEG_1704, TARGET EFI-510967) WITH BOUND D-GALACTOSE

Components

ABC transporter

Keywords

TRANSPORT PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / beta-D-galactopyranose / ABC transporter

Function and homology information

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.2 Å

Authors

Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...

Citation

Journal: To be published
Title: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM MYCOBACTERIUM SMEGMATIS (MSMEG_1704, TARGET EFI-510967) WITH BOUND D-GALACTOSE
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...

History

Deposition	Nov 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 9, 2015	Group: Data collection
Revision 1.2	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4wwh.cif.gz	385.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4wwh.ent.gz	322.5 KB	Display	PDB format
PDBx/mmJSON format	4wwh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4wwh_validation.pdf.gz	474.1 KB	Display	wwPDB validaton report
Full document	4wwh_full_validation.pdf.gz	475.4 KB	Display
Data in XML	4wwh_validation.xml.gz	35.7 KB	Display
Data in CIF	4wwh_validation.cif.gz	58.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ww/4wwh ftp://data.pdbj.org/pub/pdb/validation_reports/ww/4wwh	HTTPS FTP

-
Related structure data

Similar structure data	2gbv-1 3uug-1 3urm-1 1ozt-1 2nnx-1 2gbv-2 4oh2-1 6a9o-1 6spi-3 1uxl-1 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
Other databases	TargetTrack: EFI-510967

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: ABC transporter

B: ABC transporter

hetero molecules

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

1

A: ABC transporter

hetero molecules

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

2

B: ABC transporter

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.045, 83.617, 100.242
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

biological unit is a monomer

#1: Protein

ABC transporter / ABC transporter sugar-binding protein

Mass: 39128.242 Da / Num. of mol.: 2 / Fragment: ABC TRANSPORTER SOLUTE BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Details: (MSE)HHHHHHSSG VDLGTENLYF QS(MSE)AEGGGGG DGDAKGTVGI A(MSE)PTKSSERW VADGQN(MSE)VDQ FKAFGYDTDL QYGDDVVQNQ VSQIEN(MSE)ITK GVKLLVIAPI DGSSLTNTLQ HAADLKIPVI SYDRLIKGTP NVDYYATFDN TKVGVLQANY ...
Source: (gene. exp.)

Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_1704, MSMEI_1664 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QT42, monosaccharide-transporting ATPase

#2: Sugar

ChemComp-GAL / beta-D-galactopyranose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

#3: Chemical

ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER

Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1143 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.82 Å³/Da / Density % sol: 32.55 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein (31.9 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-galactose); Reservoir (0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000); Cryoprotection (80% Peg3350 + 20% Reservoir

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 20, 2014 / Details: MIRRORS

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.2→100.24 Å / Num. obs: 176088 / % possible obs: 98.6 % / Redundancy: 13.9 % / B_iso Wilson estimate: 7.46 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.123 / R_pim(I) all: 0.034 / Net I/σ(I): 17.2 / Num. measured all: 2440330 / Scaling rejects: 11

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	CC_1/2	R_pim(I) all	% possible all
1.2-1.22	9.1	0.854	2.7	67043	7342	0.759	0.288	84.3
6.57-100.24	12.9	0.047	57.1	16225	1254	0.999	0.013	99.9

-
Processing

Software

Name	Version	Classification
Aimless	0.1.27	data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.2→35.622 Å / FOM work R set: 0.9254 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1537	8807	5.01 %
R_work	0.1385	167151	-
obs	0.1392	175958	98.6 %

Solvent computation

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

Displacement parameters

B_iso max: 43.98 Å² / B_iso mean: 11.16 Å² / B_iso min: 2.9 Å²

Refinement step

Cycle: final / Resolution: 1.2→35.622 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4976	0	68	1143	6187
B_iso mean	-	-	8.87	22.08	-
Num. residues	-	-	-	-	658

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5220
X-RAY DIFFRACTION	f_angle_d	1.256	7135
X-RAY DIFFRACTION	f_chiral_restr	0.071	834
X-RAY DIFFRACTION	f_plane_restr	0.007	938
X-RAY DIFFRACTION	f_dihedral_angle_d	12.584	1899

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.2-1.2136	0.2732	231	0.2221	4665	4896	83
1.2136-1.2279	0.2121	264	0.2152	4884	5148	88
1.2279-1.2429	0.2267	264	0.2155	5105	5369	91
1.2429-1.2586	0.2106	292	0.2083	5380	5672	96
1.2586-1.2752	0.2069	294	0.1888	5588	5882	100
1.2752-1.2927	0.1934	290	0.1742	5604	5894	100
1.2927-1.3111	0.1968	280	0.1676	5617	5897	100
1.3111-1.3307	0.174	303	0.1627	5632	5935	100
1.3307-1.3515	0.1992	288	0.1595	5568	5856	100
1.3515-1.3737	0.1757	304	0.1549	5619	5923	100
1.3737-1.3973	0.1904	271	0.153	5617	5888	100
1.3973-1.4227	0.1687	292	0.1443	5636	5928	100
1.4227-1.4501	0.1614	299	0.142	5614	5913	100
1.4501-1.4797	0.1703	320	0.1403	5600	5920	100
1.4797-1.5119	0.1634	303	0.1335	5587	5890	100
1.5119-1.5471	0.1499	298	0.1288	5641	5939	100
1.5471-1.5857	0.1604	296	0.1271	5639	5935	100
1.5857-1.6286	0.1399	316	0.1209	5600	5916	100
1.6286-1.6765	0.1502	332	0.1224	5575	5907	100
1.6765-1.7307	0.1463	301	0.1251	5650	5951	100
1.7307-1.7925	0.147	279	0.1253	5692	5971	100
1.7925-1.8643	0.1486	313	0.1244	5631	5944	100
1.8643-1.9491	0.14	316	0.1276	5651	5967	100
1.9491-2.0519	0.1263	276	0.123	5691	5967	100
2.0519-2.1804	0.1272	293	0.1179	5664	5957	100
2.1804-2.3487	0.1314	302	0.1215	5718	6020	100
2.3487-2.585	0.1316	279	0.1254	5741	6020	100
2.585-2.9589	0.1383	301	0.1341	5746	6047	100
2.9589-3.7273	0.1458	297	0.1324	5798	6095	100
3.7273-35.6375	0.1492	313	0.1406	5998	6311	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	0.305	-0.1363	0.0507	0.4667	-0.0566	0.5296	0.0284	0.0556	-0.0462	-0.2262	-0.0083	0.0234	0.2551	-0.02	-0.028	0.1537	-0.0192	-0.0246	0.0695	0.001	0.0538	62.8982	21.7185	-1.0769
2	0.1845	0.1078	-0.001	0.3811	0.0507	0.4534	0.0162	-0.0163	0.041	0.0309	0.0083	0.0198	-0.0222	-0.0448	-0.0233	0.0393	-0.0008	0.0014	0.0508	-0.0022	0.0463	63.8389	43.7509	18.4573
3	0.2905	0.021	0.1552	0.8497	0.3406	0.6947	0.0255	-0.025	-0.0097	0.0395	-0.0057	0.0006	0.073	-0.0012	-0.0197	0.0465	-0.0015	-0.0098	0.0472	0.0026	0.0417	70.7868	28.2244	16.2767
4	0.663	-0.0011	0.1062	0.4255	0.102	0.4838	0.0461	-0.0029	-0.0748	0.0328	0.0021	-0.024	0.1758	-0.0602	-0.0297	0.0764	-0.0327	-0.0126	0.0795	0.0173	0.0513	65.6368	24.0098	18.1198
5	0.6406	-0.071	-0.1378	1.3226	0.186	0.7844	-0.0046	-0.0066	0.0835	0.0425	-0.0026	0.0215	-0.1057	0.0581	0.0075	0.0677	-0.0072	0.0001	0.0631	-0.0007	0.0706	66.5418	67.1956	-4.212
6	0.2559	0.0156	-0.0143	0.9241	-0.2203	0.248	0.0255	-0.0563	0.0618	0.1576	-0.0027	0.1027	-0.1167	0.0252	-0.0222	0.1016	0.0071	0.0189	0.0693	-0.0018	0.0717	62.0144	63.7747	4.705
7	0.2328	0.024	-0.1247	0.5053	0.0727	0.5036	0.0088	0.0087	0.0262	0.0144	-0.0014	0.1078	-0.0354	-0.0644	-0.0115	0.0283	0.0058	0.0099	0.0456	0.0025	0.0697	55.534	59.4097	-7.7613
8	0.3482	-0.214	-0.146	0.563	0.4504	0.8623	0.0016	0.0416	-0.029	-0.0928	-0.0054	0.0221	-0.0224	0.0212	-0.0178	0.0599	-0.007	0.0002	0.0469	-0.0042	0.0411	63.7005	40.367	-23.6301
9	0.1033	0.1442	0.2803	1.2411	1.2579	1.4752	-0.0018	0.0426	-0.0779	0.0278	-0.0137	0.0595	0.153	-0.0431	0.0185	0.0719	-0.0056	-0.0101	0.07	-0.0038	0.0743	56.0746	45.2583	-21.8643
10	0.3872	0.146	0.2235	0.6533	0.5367	0.7976	0.0028	0.0058	-0.032	0.0044	-0.0092	0.0286	0.0451	-0.0447	0.0081	0.047	-0.0063	-0.0002	0.049	0.0021	0.0485	60.908	38.2794	-16.2036
11	0.4869	-0.0305	-0.0396	0.405	0.3317	1.1997	0.0083	-0.0016	-0.1033	0.0116	0.0427	-0.0567	0.1814	0.092	-0.0454	0.066	0.0064	0.0018	0.0541	-0.0086	0.0633	70.0106	35.3198	-16.411
12	0.3933	-0.4625	-0.3421	0.5444	0.4067	0.5209	-0.0213	0.0285	-0.0573	-0.0156	0.0124	-0.1269	0.0494	0.0857	0.0018	0.043	0.0123	0.0183	0.0583	-0.0132	0.0816	77.5108	38.912	-18.2072
13	0.2832	-0.0054	-0.0448	0.5039	0.1772	0.3265	0.0006	0.0211	0.0242	-0.0585	0.0052	-0.0152	-0.0469	0.0122	-0.0063	0.0416	-0.0057	0.0076	0.0473	-0.0006	0.0436	68.8495	59.7626	-16.1452
14	0.6175	0.2253	-0.1979	0.9413	-0.182	0.5839	-0.0113	-0.0028	0.0229	-0.074	0.0379	0.1713	-0.0194	-0.0922	-0.0067	0.0386	0.0088	-0.0018	0.0749	0.0094	0.1031	48.9971	63.455	-14.0498
15	1.1648	-0.0017	0.129	0.7043	0.1465	0.6969	-0.0226	0.0516	-0.0025	-0.0506	0.0144	-0.1575	0.0034	0.1078	0.0118	0.0764	-0.0105	0.023	0.075	0.0098	0.0801	77.078	61.0012	-22.3363

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 37 through 125 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 126 through 270 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 271 through 314 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 315 through 365 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 37 through 66 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 67 through 92 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 93 through 158 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 159 through 178 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 179 through 197 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 198 through 219 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 220 through 247 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 248 through 270 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 271 through 315 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 316 through 339 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 340 through 365 )	B

-
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://pdbjlvh1.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