PDB-4gd5: X-ray Crystal Structure of a Putative Phosphate ABC Transporter S...

ID or keywords:

Entry

Database: PDB / ID: 4gd5

Title

X-ray Crystal Structure of a Putative Phosphate ABC Transporter Substrate-Binding Protein with Bound Phosphate from Clostridium perfringens

Components

Phosphate ABC transporter, phosphate-binding protein

Keywords

TRANSPORT PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / phosphate ABC transporter / phosphate-binding protein

Function / homology

Function and homology information

phosphate ion transport / phosphate ion binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Clostridium perfringens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: X-ray Crystal Structure of a Putative Phosphate ABC Transporter Substrate-Binding Protein with Bound Phosphate from Clostridium perfringens
Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases

History

Deposition	Jul 31, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2013	Group: Other

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gd5.cif.gz	209.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4gd5.ent.gz	177.6 KB	Display	PDB format
PDBx/mmJSON format	4gd5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gd5_validation.pdf.gz	448.4 KB	Display	wwPDB validaton report
Full document	4gd5_full_validation.pdf.gz	449.1 KB	Display
Data in XML	4gd5_validation.xml.gz	26.1 KB	Display
Data in CIF	4gd5_validation.cif.gz	40.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gd/4gd5 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/4gd5	HTTPS FTP

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Related structure data

Similar structure data	5me4-d 4twj-d 5h3j-d 2h2f-d 4gvp-3 3gzg-3 4gvp-1 3n6u-d 2h4h-d 4k3f-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP04389

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Phosphate ABC transporter, phosphate-binding protein

B: Phosphate ABC transporter, phosphate-binding protein

hetero molecules

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

1

A: Phosphate ABC transporter, phosphate-binding protein

hetero molecules

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

2

B: Phosphate ABC transporter, phosphate-binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.888, 73.302, 56.415
Angle α, β, γ (deg.)	90.00, 102.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Phosphate ABC transporter, phosphate-binding protein Mass: 29998.979 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / Gene: CPF_0617, pstS / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q0TTH0, UniProt: A0A0H2YSI2*PLUS

#1: Protein

Phosphate ABC transporter, phosphate-binding protein

Mass: 29998.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium perfringens (bacteria) / Strain: ATCC 13124 / Gene: CPF_0617, pstS / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q0TTH0, UniProt: A0A0H2YSI2*PLUS

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Non-polymers , 5 types, 689 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 681 / 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: 1.88 Å³/Da / Density % sol: 34.69 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25%PEG 3350, 0.2M NaBr, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2012 / Details: Be Lens
Radiation	Monochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.7→30 Å / Num. all: 49208 / Num. obs: 49208 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / B_iso Wilson estimate: 15.49 Å² / R_merge(I) obs: 0.086 / Net I/σ(I): 21.7
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.628 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2427 / % possible all: 100

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Processing

Software

Name	Version	Classification
BLU-MAX		data collection
PHENIX		model building
BUSTER	2.10.0	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→28.07 Å / Cor.coef. F_o:F_c: 0.9604 / Cor.coef. F_o:F_c free: 0.943 / SU R Cruickshank DPI: 0.103 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1857	2349	5.07 %	RANDOM
R_work	0.1505	-	-	-
all	0.1523	49208	-	-
obs	0.1523	46348	94.6 %	-

Displacement parameters

B_iso mean: 18.62 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.0328 Å²	0 Å²	0.0865 Å²
2-	-	-0.8149 Å²	0 Å²
3-	-	-	-0.2179 Å²

Refine analyze

Luzzati coordinate error obs: 0.165 Å

Refinement step

Cycle: LAST / Resolution: 1.7→28.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3670	0	25	681	4376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	3837	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.03	5184	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d	2.75	1849	SINUSOIDAL	2
X-RAY DIFFRACTION	t_omega_torsion	3.73
X-RAY DIFFRACTION	t_other_torsion	2.75

LS refinement shell

Resolution: 1.7→1.74 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2034	128	5.51 %
R_work	0.1743	2193	-
all	0.1759	2321	-
obs	-	2193	94.6 %

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	0.7621	0.5768	0.6973	0.1839	-0.425	2.3163	-0.0146	0.2128	-0.1977	-0.0648	0.1447	-0.0418	0.0525	0.2186	-0.1301	-0.0328	-0.0139	0	0.014	-0.0447	-0.0549	-10.0277	42.5224	23.6267
2	0.1248	1.1702	-0.5018	0	1.7806	1.965	-0.0426	0.2831	-0.1607	-0.135	0.1178	-0.097	0.0409	0.0598	-0.0752	0.0569	-0.0465	0.0064	0.0913	-0.0532	-0.0182	-4.7932	44.1487	22.0796
3	2.6575	-0.1445	-0.4879	1.2319	-0.0606	1.3595	-0.0749	-0.0083	0.1456	-0.0685	0.0658	0.0561	-0.0427	0.0909	0.0092	-0.0232	-0.0445	0.0023	-0.0557	-0.0056	-0.0624	-5.9017	53.4217	33.5216
4	2.7132	0.3106	0.3464	2.7626	-0.296	1.3531	-0.1024	-0.2791	0.4079	-0.1312	0.0069	0.0936	-0.1817	-0.0703	0.0955	-0.0068	-0.0072	0.013	-0.0097	-0.0438	-0.0133	-14.0362	55.7122	35.9631
5	1.2226	0.1169	0.399	0.8214	-0.8299	1.6457	0.0202	-0.0808	-0.072	0.0304	-0.0384	-0.0028	-0.0646	0.0558	0.0181	-0.0155	-0.0086	0.0049	-0.0151	0.0135	-0.0314	-11.0179	35.9183	55.2445
6	0.2775	-1.0837	-0.8599	2.9369	0.3477	2.1602	0.025	-0.3665	0.3704	0.0321	0.0361	-0.3378	-0.2671	0.2752	-0.0611	0.0181	-0.0663	0.003	0.057	-0.0163	0.0145	-7.0383	46.2396	55.5335
7	0.7721	-0.1698	0.5388	0.3118	-0.5601	1.4666	0.039	0.0967	-0.1328	-0.0874	-0.0276	-0.0077	0.1319	0.1025	-0.0114	-0.0179	0.0062	0.006	-0.0246	-0.0036	-0.0195	-11.4149	33.0107	46.0506
8	1.7256	1.182	-1.7165	1.3354	-1.6693	2.9915	0.0468	-0.0158	0.1004	0.0029	0.124	0.1935	-0.1338	-0.0643	-0.1707	-0.0263	-0.0065	0.0121	-0.06	0.0273	-0.0335	-20.2142	46.0755	39.6303
9	0.9353	0.895	-0.834	4.8873	-0.9022	1.9889	0.0445	0.3858	0.2627	-0.2097	0.0187	0.1465	-0.3826	0.0914	-0.0632	0.1208	-0.0318	-0.0177	0.0154	0.019	0.0021	-11.7582	54.7446	20.0995
10	4.1375	0.3812	0.5968	1.5199	-0.5787	5.4765	0.0764	0.0767	-0.302	-0.066	-0.0397	-0.0064	0.1659	-0.2369	-0.0366	-0.0123	-0.033	-0.023	-0.0261	-0.026	0	-21.623	41.1886	27.6523
11	0.7484	0.2371	-1.9386	0.9341	-0.2536	1.7895	-0.0661	0.3184	0.2265	-0.1685	0.0387	0.0108	0.0213	-0.3092	0.0274	-0.0367	-0.0155	0.0036	0.06	0.0384	-0.0688	13.652	60.5674	24.5532
12	0.8973	0.0715	-2.1941	1.3244	0.5665	0.9303	-0.05	0.1174	0.1876	-0.1264	0.1237	0.0164	0.1408	-0.2104	-0.0736	0.0148	-0.0205	0.0163	0.0899	0.0479	-0.0646	11.4369	59.9507	19.2162
13	2.9042	-0.2753	0.4123	1.048	0.2801	0.3442	-0.0688	0.1421	-0.225	-0.0827	0.0984	-0.0301	-0.0061	-0.0879	-0.0296	0.0002	-0.0365	0.009	-0.0234	-0.0147	-0.0234	9.8996	50.1039	33.5217
14	2.7904	0.4832	-0.6828	2.3935	-0.2399	1.7907	-0.101	-0.2043	-0.3935	-0.0474	0.0682	-0.1389	0.3266	0.0396	0.0328	0.026	0.005	-0.0059	-0.0209	0.0118	-0.0022	17.5467	46.3984	35.5933
15	1.2835	0.2546	-0.0875	0.7511	0.8851	1.7577	0.0331	-0.0922	0.0324	0.0671	-0.0334	-0.0619	0.1002	-0.0085	0.0003	-0.0143	0.0006	-0.0055	-0.0353	-0.006	-0.0351	15.4036	66.7427	55.2578
16	1.7382	-0.6957	0.0385	0.951	0.1268	1.51	0.0123	0.0381	-0.0014	0.0389	-0.0363	-0.0532	0.0484	-0.0734	0.024	-0.0087	0.0015	0.0006	-0.0214	-0.0083	-0.0296	12.2914	65.9972	49.0461
17	2.8134	0.6239	-1.4985	1.01	1.9508	3.7417	-0.0187	0.1073	-0.0758	-0.0331	0.1436	-0.0339	0.0296	-0.0254	-0.1248	-0.0476	0.0067	-0.0083	0.0001	-0.0496	0.0193	29.9067	64.6925	46.3774
18	1.3642	-0.0628	-0.4958	0.6328	-1.1833	0.0768	-0.0551	0.0227	-0.1231	-0.1598	0.1003	-0.1222	0.2207	-0.0063	-0.0452	0.0428	-0.0113	0.0064	-0.0128	-0.0168	0.0051	17.7739	50.3852	32.6788
19	2.9986	0.175	-0.1187	1.2905	-0.0595	1.8199	-0.0571	0.4034	0.0146	-0.1332	0.05	-0.2001	0.1365	0.09	0.0071	-0.0162	-0.0122	0.0379	0.0461	0.0263	-0.0647	22.3392	56.836	21.3381
20	1.8615	2.9336	-0.8049	1.4432	-1.8244	7.6092	-0.07	0.0879	0.5304	-0.2274	0.0249	0.117	-0.1545	0.1221	0.0451	-0.0448	-0.0323	0.0122	-0.0353	-0.0156	0.0218	25.9213	63.7314	31.9836

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|34 - A\|59 }	A	34 - 59
2	X-RAY DIFFRACTION	2	{ A\|60 - A\|69 }	A	60 - 69
3	X-RAY DIFFRACTION	3	{ A\|70 - A\|92 }	A	70 - 92
4	X-RAY DIFFRACTION	4	{ A\|93 - A\|108 }	A	93 - 108
5	X-RAY DIFFRACTION	5	{ A\|109 - A\|165 }	A	109 - 165
6	X-RAY DIFFRACTION	6	{ A\|166 - A\|181 }	A	166 - 181
7	X-RAY DIFFRACTION	7	{ A\|182 - A\|224 }	A	182 - 224
8	X-RAY DIFFRACTION	8	{ A\|225 - A\|243 }	A	225 - 243
9	X-RAY DIFFRACTION	9	{ A\|244 - A\|255 }	A	244 - 255
10	X-RAY DIFFRACTION	10	{ A\|256 - A\|276 }	A	256 - 276
11	X-RAY DIFFRACTION	11	{ B\|34 - B\|57 }	B	34 - 57
12	X-RAY DIFFRACTION	12	{ B\|58 - B\|68 }	B	58 - 68
13	X-RAY DIFFRACTION	13	{ B\|69 - B\|92 }	B	69 - 92
14	X-RAY DIFFRACTION	14	{ B\|93 - B\|108 }	B	93 - 108
15	X-RAY DIFFRACTION	15	{ B\|109 - B\|165 }	B	109 - 165
16	X-RAY DIFFRACTION	16	{ B\|166 - B\|215 }	B	166 - 215
17	X-RAY DIFFRACTION	17	{ B\|216 - B\|232 }	B	216 - 232
18	X-RAY DIFFRACTION	18	{ B\|233 - B\|247 }	B	233 - 247
19	X-RAY DIFFRACTION	19	{ B\|248 - B\|266 }	B	248 - 266
20	X-RAY DIFFRACTION	20	{ B\|267 - B\|276 }	B	267 - 276

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