PDB-4i1d: The crystal structure of an ABC transporter substrate-binding pro...

ID or keywords:

Entry

Database: PDB / ID: 4i1d

Title

The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110

Components

ABC transporter substrate-binding protein

Keywords

TRANSPORT PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

Function and homology information

periplasmic space
Similarity search - Function

Biological species

Bradyrhizobium japonicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.201 Å

Authors

Fan, Y. / Tan, K. / Mack, J. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Proteins / Year: 2013
Title: Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-Coumaric acid and related aromatic acids.
Authors: Tan, K. / Chang, C. / Cuff, M. / Osipiuk, J. / Landorf, E. / Mack, J.C. / Zerbs, S. / Joachimiak, A. / Collart, F.R.

History

Deposition	Nov 20, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 5, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2013	Group: Database references
Revision 1.2	Sep 25, 2013	Group: Database references
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4i1d.cif.gz	519.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4i1d.ent.gz	431.8 KB	Display	PDB format
PDBx/mmJSON format	4i1d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4i1d_validation.pdf.gz	520.3 KB	Display	wwPDB validaton report
Full document	4i1d_full_validation.pdf.gz	535.8 KB	Display
Data in XML	4i1d_validation.xml.gz	57.9 KB	Display
Data in CIF	4i1d_validation.cif.gz	74.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i1/4i1d ftp://data.pdbj.org/pub/pdb/validation_reports/i1/4i1d	HTTPS FTP

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Related structure data

Related structure data	3rpwC 3sg0C 3tx6C 3uk0C 3ukjC 4dqdC 4eyoC 4eyqC 4f8jC 4fb4C 4fcl PDB Unreleased entry C: citing same article (ref.)
Similar structure data	1lvc-d 3git-d 5vlb-d 1k90-d 30218 5v4m-d 1k93-d 6hz4-d 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
Other databases	TargetTrack: MCSG-APC102202

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (1)

Deposited unit

A: ABC transporter substrate-binding protein

B: ABC transporter substrate-binding protein

C: ABC transporter substrate-binding protein

D: ABC transporter substrate-binding protein

hetero molecules

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

1

A: ABC transporter substrate-binding protein

B: ABC transporter substrate-binding protein

C: ABC transporter substrate-binding protein

D: ABC transporter substrate-binding protein

hetero molecules

A: ABC transporter substrate-binding protein

B: ABC transporter substrate-binding protein

C: ABC transporter substrate-binding protein

D: ABC transporter substrate-binding protein

hetero molecules

defined by software
298 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	136.641, 136.641, 185.634
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

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Protein , 1 types, 4 molecules ABCD

#1: Protein	ABC transporter substrate-binding protein Mass: 35735.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bll6825 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q89F76

#1: Protein

ABC transporter substrate-binding protein

Mass: 35735.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bll6825 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q89F76

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Non-polymers , 5 types, 315 molecules

#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₅
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	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: 3.5 Å³/Da / Density % sol: 64.85 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2M Lithium Sulfate, 0.1M Sodium Acetate:Acetic Acid:HCl, 50% (v/v) PEG400, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2011 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97921 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 100645 / Num. obs: 100645 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / R_merge(I) obs: 0.094 / Net I/σ(I): 31.5
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.545 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4572 / % possible all: 90.2

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
ARP		model building
WARP		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.201→49.892 Å / SU ML: 0.63 / σ(F): 1.35 / Phase error: 24.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2092	5020	4.99 %	random
R_work	0.172	-	-	-
all	0.1739	100533	-	-
obs	0.1739	100533	98.76 %	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.608 Å² / k_sol: 0.358 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.5273 Å²	-0 Å²	-0 Å²
2-	-	7.5273 Å²	0 Å²
3-	-	-	-15.0546 Å²

Refinement step

Cycle: LAST / Resolution: 2.201→49.892 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9926	0	372	243	10541

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10551
X-RAY DIFFRACTION	f_angle_d	1.026	14370
X-RAY DIFFRACTION	f_dihedral_angle_d	14.421	3766
X-RAY DIFFRACTION	f_chiral_restr	0.067	1514
X-RAY DIFFRACTION	f_plane_restr	0.005	1851

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 (%)
2.2011-2.2261	0.3683	153	0.2869	2726	X-RAY DIFFRACTION	86
2.2261-2.2523	0.3338	168	0.2684	2927	X-RAY DIFFRACTION	92
2.2523-2.2797	0.3149	160	0.2532	3062	X-RAY DIFFRACTION	95
2.2797-2.3086	0.3112	157	0.2489	3099	X-RAY DIFFRACTION	97
2.3086-2.339	0.3267	166	0.2396	3074	X-RAY DIFFRACTION	98
2.339-2.371	0.2786	150	0.2192	3207	X-RAY DIFFRACTION	99
2.371-2.4049	0.2842	159	0.2185	3187	X-RAY DIFFRACTION	100
2.4049-2.4408	0.2606	143	0.219	3227	X-RAY DIFFRACTION	100
2.4408-2.4789	0.2647	200	0.2167	3166	X-RAY DIFFRACTION	100
2.4789-2.5196	0.2525	158	0.2164	3178	X-RAY DIFFRACTION	100
2.5196-2.563	0.2719	165	0.2093	3210	X-RAY DIFFRACTION	100
2.563-2.6096	0.2661	175	0.2085	3163	X-RAY DIFFRACTION	100
2.6096-2.6598	0.2663	158	0.198	3242	X-RAY DIFFRACTION	100
2.6598-2.7141	0.216	160	0.1967	3192	X-RAY DIFFRACTION	100
2.7141-2.7731	0.2562	148	0.1981	3224	X-RAY DIFFRACTION	100
2.7731-2.8376	0.2192	175	0.1985	3213	X-RAY DIFFRACTION	100
2.8376-2.9085	0.2533	179	0.2085	3199	X-RAY DIFFRACTION	100
2.9085-2.9872	0.2512	164	0.2089	3198	X-RAY DIFFRACTION	100
2.9872-3.0751	0.2524	169	0.2114	3217	X-RAY DIFFRACTION	100
3.0751-3.1743	0.2558	154	0.1988	3249	X-RAY DIFFRACTION	100
3.1743-3.2877	0.2341	179	0.1901	3203	X-RAY DIFFRACTION	100
3.2877-3.4193	0.2203	166	0.1847	3231	X-RAY DIFFRACTION	100
3.4193-3.5749	0.2001	170	0.1609	3202	X-RAY DIFFRACTION	100
3.5749-3.7633	0.1741	199	0.1471	3224	X-RAY DIFFRACTION	100
3.7633-3.999	0.1679	187	0.137	3212	X-RAY DIFFRACTION	100
3.999-4.3076	0.1624	172	0.1316	3246	X-RAY DIFFRACTION	100
4.3076-4.7408	0.1458	173	0.1241	3248	X-RAY DIFFRACTION	99
4.7408-5.4261	0.1857	157	0.1419	3285	X-RAY DIFFRACTION	100
5.4261-6.8336	0.1823	168	0.159	3329	X-RAY DIFFRACTION	100
6.8336-49.9051	0.1994	188	0.1674	3373	X-RAY DIFFRACTION	98

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	4.0038	0.1549	2.1033	4.7306	-2.2747	2.511	0.1589	-0.1029	0.2114	-0.07	-0.0171	0.2977	0.0265	-0.078	-0.1084	0.3203	0.0311	0.0837	0.3633	-0.014	0.4192	-1.0866	88.3287	10.6974
2	0.8093	0.1345	0.3902	0.844	0.5284	3.3625	0.0351	-0.136	-0.1118	0.1867	-0.0803	-0.1177	0.1823	0.0912	0.03	0.4014	0.04	0.028	0.4179	0.0676	0.4562	5.8511	88.8232	34.2803
3	0.7399	0.1587	0.0192	1.2533	0.0315	4.4453	-0.0559	0.0324	-0.1079	-0.0087	-0.0916	-0.2962	0.6443	0.2014	0.1406	0.3431	0.0294	0.075	0.2926	0.0207	0.432	5.0328	81.6161	22.9978
4	4.1806	0.4198	1.6266	2.941	2.7128	4.4539	0.0885	-0.0532	-0.0156	0.0502	0.1131	-0.2256	0.1094	0.4037	-0.1614	0.3415	-0.0406	0.0621	0.3537	-0.0074	0.3431	-34.1673	81.3865	29.3023
5	0.6948	-0.7724	0.0121	2.6189	-0.337	1.8415	0.0252	0.1539	0.0179	-0.3154	-0.0026	-0.1115	-0.1875	-0.064	-0.026	0.3768	-0.0496	0.0258	0.3151	-0.0334	0.2753	-41.5949	98.8224	9.4549
6	0.6052	0.2773	-0.0833	2.0513	-0.53	1.9272	0.0036	-0.0914	0.0546	-0.214	-0.091	-0.0664	0.2014	0.0505	0.0568	0.3219	-0.018	0.0544	0.3145	-0.062	0.3457	-38.8839	83.9875	17.1012
7	7.5594	-0.3026	3.5603	4.3993	-1.3736	7.934	-0.0655	-0.6066	0.0208	-0.0283	-0.0012	0.225	0.8462	-0.2671	0.1418	0.3946	-0.0542	0.0724	0.3697	0.04	0.3273	19.1733	99.4048	10.795
8	0.7802	0.4012	-1.0883	3.2392	-0.8154	5.8971	0.0659	-0.2575	-0.0695	0.3029	-0.0493	0.0346	-0.2632	0.1527	-0.0221	0.3249	-0.0058	0.0366	0.4533	0.0397	0.3678	18.6915	110.7585	19.6237
9	3.8056	-0.4296	0.9242	0.7205	-0.2457	1.9239	0.047	0.339	0.209	0.0718	-0.0245	0.0562	-0.1201	0.105	0.0116	0.4109	-0.0051	0.0074	0.417	0.0486	0.3761	14.0034	115.309	5.0808
10	3.8013	1.9435	1.8459	4.7709	2.0892	3.1837	-0.2499	0.3076	0.1857	-0.3587	0.1313	0.5042	-0.3335	-0.1233	0.1394	0.3536	0.0679	-0.006	0.4525	0.0487	0.3943	-7.7556	120.9012	3.4876
11	3.1831	-0.222	1.0532	1.0662	-0.0606	2.2942	-0.1021	0.0858	-0.2824	-0.0334	0.0904	0.1884	0.0561	-0.2322	-0.0062	0.4051	0.003	0.0816	0.4244	0.0203	0.4261	1.2187	108.1945	4.748
12	1.1527	-0.4896	0.3505	1.5367	-1.5108	4.1784	0.0489	0.322	0.0679	-0.1573	-0.1516	-0.1172	0.2035	0.2019	0.0801	0.3871	-0.0121	0.0937	0.3719	0.0021	0.3794	18.6447	107.6803	-0.3468
13	6.3515	-0.3317	0.5045	3.4474	2.0106	4.8925	-0.1595	-0.7286	-0.0593	0.5442	0.0262	0.1073	0.2498	0.1593	0.1627	0.4871	0.1011	0.0388	0.3735	0.037	0.3738	1.0419	122.7628	15.3673
14	1.1742	-0.4348	-0.5115	3.5802	-1.9693	5.1303	-0.1374	0.118	-0.0744	-0.1044	0.0947	-0.2184	0.1678	-0.1428	0.0139	0.3947	-0.0367	0.058	0.3321	-0.0498	0.3221	-52.252	97.6449	32.8185
15	3.6379	0.8509	-2.3305	6.4597	-2.7574	7.8076	0.1066	0.2434	0.1388	0.1907	0.1601	0.0659	-0.7565	-0.5673	-0.2731	0.3408	0.0435	0.0074	0.3417	0.0013	0.2669	-56.0771	107.8078	41.3079
16	5.944	-1.3101	1.4264	1.7866	-0.1488	2.4256	0.0526	-0.4606	-0.01	0.2148	0.0541	-0.1602	0.0766	-0.0242	-0.1095	0.4689	-0.019	-0.0081	0.32	0.019	0.269	-35.9106	97.9679	54.3774
17	4.2808	-2.2231	0.4854	4.4681	1.4101	3.2563	-0.2189	-0.2376	0.0664	0.1898	0.1603	-0.3018	-0.2003	0.1615	0.0474	0.3746	-0.0546	-0.015	0.3495	0.0176	0.3931	-29.1685	108.4061	52.2595
18	5.4397	-2.0034	-2.2099	2.1082	0.1801	7.9575	-0.2059	0.3127	-0.3718	0.0334	0.074	-0.053	0.2681	0.1272	0.1321	0.3704	-0.067	0.0223	0.3387	-0.0253	0.4149	-30.6385	91.2531	48.1932
19	2.7908	0.3643	1.9361	1.0205	-0.0916	4.9846	0.0163	-0.3042	-0.2061	0.0467	0.0154	0.0033	0.3798	-0.5033	-0.0759	0.331	-0.0429	0.0594	0.3115	0.0017	0.31	-53.2764	93.9922	47.7877
20	6.7585	-0.0478	0.5445	4.2028	0.3066	2.3597	-0.2951	0.6671	0.0701	-0.4743	0.2378	-0.0629	-0.256	-0.168	0.0679	0.494	-0.0948	-0.0171	0.2885	-0.0078	0.2695	-36.0631	112.4968	46.2388

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 43:124)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 125:281)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 282:363)
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 42:128)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 129:266)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 267:363)
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 42:70)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 71:128)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 129:152)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 153:224)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 225:281)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 282:337)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 338:364)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq 44:98)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 99:128)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 129:176)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 177:224)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 225:266)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 267:337)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 338:363)

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Protein , 1 types, 4 molecules ABCD

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

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-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 315 molecules

-
Details

-
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

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Yorodumi