PDB-4kd5: substrate binding domain of putative molybdenum ABC transporter f...

ID or keywords:

Entry

Database: PDB / ID: 4kd5

Title

substrate binding domain of putative molybdenum ABC transporter from Clostridium difficile

Components

ABC-type transport system, molybdenum-specific extracellular solute-binding protein

Keywords

TRANSPORT PROTEIN /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha fold /

ABC transporter

Function / homology

Function and homology information

molybdate ion transport /

metal ion binding
Similarity search - Function

Biological species

Clostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.4999 Å

Authors

Maltseva, N. / Kim, Y. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: Substrate binding domain of putative molybdenum ABC transporter from Clostridium difficile 630
Authors: Maltseva, N. / Kim, Y. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Apr 24, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4kd5.cif.gz	365.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4kd5.ent.gz	316.2 KB	Display	PDB format
PDBx/mmJSON format	4kd5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kd/4kd5 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/4kd5	HTTPS FTP

-
Related structure data

Similar structure data	6xp0-d 5uax-d 2izz-d 6xoz-d 5uav-d 6xp3-d 6xp2-d 5uau-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) 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: IDP05504

Similar structure data

Other databases

TargetTrack: IDP05504

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

C: ABC-type transport system, molybdenum-specific extracellular solute-binding protein

A: ABC-type transport system, molybdenum-specific extracellular solute-binding protein

B: ABC-type transport system, molybdenum-specific extracellular solute-binding protein

D: ABC-type transport system, molybdenum-specific extracellular solute-binding protein

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

C: ABC-type transport system, molybdenum-specific extracellular solute-binding protein

hetero molecules

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

3

A: ABC-type transport system, molybdenum-specific extracellular solute-binding protein

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

4

B: ABC-type transport system, molybdenum-specific extracellular solute-binding protein

hetero molecules

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

5

D: ABC-type transport system, molybdenum-specific extracellular solute-binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.644, 141.068, 122.590
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	ABC-type transport system, molybdenum-specific extracellular solute-binding protein Mass: 25732.570 Da / Num. of mol.: 4 / Fragment: ModA (UNP Residues 42-270) / Mutation: delta 41 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_08690, modA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q18A64
#2: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-SBT / 2-BUTANOL / 2-Butanol Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.6 Å³/Da / Density % sol: 52.63 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 2.4M ammonium sulfate, 150 mM Formate pH 4.0, 3% 2-Butanol, 3mM rhenium chloride , VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2013 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97899 Å / Relative weight: 1
Reflection	Resolution: 2.4999→50 Å / Num. all: 37152 / Num. obs: 37152 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / B_iso Wilson estimate: 58.32 Å² / R_sym value: 0.08 / Net I/σ(I): 15.3
Reflection shell	Resolution: 2.4999→2.54 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.03 / Num. unique all: 1831 / R_sym value: 0.782 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELX		model building
RESOLVE		model building
BUCCANEER		model building
PHENIX	(phenix.refine: dev_1227)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
RESOLVE		phasing
BUCCANEER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.4999→34.089 Å / SU ML: 0.35 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.6 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	1946	5.37 %	random
R_work	0.204	-	-	-
all	0.207	36246	-	-
obs	0.207	36246	96.99 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 64.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.4999→34.089 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7032	0	34	82	7148

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7208
X-RAY DIFFRACTION	f_angle_d	0.789	9698
X-RAY DIFFRACTION	f_dihedral_angle_d	17.119	2724
X-RAY DIFFRACTION	f_chiral_restr	0.054	1142
X-RAY DIFFRACTION	f_plane_restr	0.003	1230

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
2.4999-2.5624	0.3708	129	0.3142	2226	2255	89
2.5624-2.6317	0.3738	135	0.2822	2338	2473	94
2.6317-2.7091	0.2906	128	0.3002	2361	2489	94
2.7091-2.7965	0.3604	134	0.2969	2375	2509	95
2.7965-2.8964	0.3974	132	0.2854	2411	2543	97
2.8964-3.0123	0.3701	142	0.2698	2466	2608	97
3.0123-3.1493	0.3352	141	0.2653	2481	2622	99
3.1493-3.3152	0.3122	142	0.2455	2459	2601	99
3.3152-3.5227	0.252	144	0.2168	2508	2652	99
3.5227-3.7944	0.2616	142	0.1898	2510	2652	100
3.7944-4.1756	0.277	143	0.1701	2527	2670	100
4.1756-4.7784	0.1875	145	0.145	2529	2674	99
4.7784-6.0149	0.2131	146	0.1683	2564	2710	100
6.0149-34.0927	0.2129	143	0.1951	2545	2688	95

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	4.2665	0.7059	-0.8315	1.728	0.1214	6.4909	0.1516	0.0755	0.2743	-0.0452	-0.1514	0.459	-0.1308	-0.4252	0.0092	0.4555	0.1302	-0.094	0.2956	-0.0176	0.5121	78.5182	73.2332	19.9175
2	8.0987	1.8994	2.9884	8.3915	0.9643	3.8208	-0.1888	0.4229	0.2767	-0.5656	-0.0893	0.1985	-0.5872	-0.0071	0.2608	0.5916	0.2127	0.0336	0.3955	0.0225	0.3123	70.3149	95.7244	0.2516
3	2.2548	-2.1094	1.8774	5.1405	-4.0828	4.1236	0.3928	0.4082	-0.2622	-0.3846	-0.2913	-0.1901	0.038	0.3019	-0.1266	0.4945	0.1563	-0.0294	0.3945	-0.0758	0.4457	81.7317	80.0491	9.0143
4	3.1856	1.6289	0.0654	1.7488	-0.8978	9.203	0.1746	0.1843	-0.034	-0.2363	-0.5899	-0.5353	-0.1245	0.8335	0.4102	0.4558	0.1831	-0.0078	0.5009	0.051	0.5888	105.7179	55.0782	19.3704
5	7.4918	-1.8259	-3.2856	4.066	1.5271	2.6351	0.1896	0.6323	0.1146	-0.484	-0.1141	0.1503	-0.1102	-0.164	-0.0726	0.7102	0.3315	-0.0997	0.5986	-0.0064	0.4419	111.0723	35.0374	0.3139
6	4.007	0.705	1.9793	4.9815	1.179	7.3398	0.1415	0.1033	0.171	-0.5438	-0.369	0.6139	-0.4853	-0.8087	0.2317	0.4682	0.1718	-0.0083	0.3644	0.0031	0.4927	97.8051	53.7414	14.6904
7	3.1251	1.9567	-3.0661	6.11	-0.8944	3.5963	0.2805	-0.4027	-1.2226	0.885	-0.4328	-0.7702	0.5627	0.6683	0.2451	0.7338	0.0019	-0.1971	0.5208	0.07	0.7561	75.4372	66.8251	43.8034
8	4.3055	0.7814	-3.0618	7.4069	-1.3382	3.3343	0.9481	-1.1594	-0.4549	0.6523	-1.0622	0.8831	0.3899	-0.0444	0.0787	0.7184	-0.2399	-0.1521	0.6643	-0.0422	0.6583	68.4703	77.8478	48.7893
9	6.7604	1.3035	-0.6928	7.987	1.2135	7.922	0.4282	-0.0818	-0.1212	0.3125	-0.2834	-0.9663	0.0708	0.985	-0.1457	0.3129	-0.0496	-0.103	0.5426	0.0569	0.5037	94.4989	91.5687	40.0308
10	4.3431	1.3031	-0.6508	2.4245	-0.8684	2.0978	0.6716	-1.0091	-1.353	0.5302	-0.4342	-0.5807	0.5965	-0.2147	-0.2203	0.8292	-0.231	-0.3255	0.7685	0.2896	0.808	80.7738	75.5762	52.029
11	2.0454	2.9415	1.487	2.0483	2.9615	4.2412	-0.1321	0.0953	1.4665	0.1806	-0.3258	0.711	-0.8619	-0.4102	0.4747	0.7482	0.1188	-0.1048	0.6481	-0.0885	0.8488	105.5362	62.3204	43.9668
12	7.7419	0.7221	1.4345	5.2431	0.6332	9.9815	-0.1679	0.2262	0.4782	0.2556	-0.2424	-0.3033	-0.4657	1.1921	0.3274	0.4896	-0.0257	-0.1434	0.6201	0.0454	0.5702	117.4132	53.4438	43.2937
13	7.3263	3.6029	2.2099	6.5018	1.9362	2.6733	0.1356	-0.8933	0.1943	0.4159	-0.3376	0.7816	-0.3052	-1.2678	0.1154	0.5634	0.0077	0.2624	0.9742	-0.0252	0.6984	90.9059	39.0503	46.2856
14	4.573	-0.7825	6.6572	4.0391	-0.6952	9.758	0.3026	-0.328	-0.2515	-0.1284	-0.2197	0.0605	0.5504	-0.5187	-0.0757	0.4006	0.0905	0.0806	0.5336	0.0151	0.4073	94.744	29.5169	38.1609
15	8.4902	0.8926	1.3884	6.2918	1.3905	9.1683	0.1951	-0.4601	0.5845	0.0714	-0.396	1.1314	-0.6801	-1.4893	0.2447	0.4475	0.1354	0.0468	0.6423	-0.0785	0.6396	88.7645	41.9021	38.6385
16	4.0668	0.7591	-1.0177	3.7886	0.1453	1.7179	0.1718	-0.9136	0.4211	0.6618	-0.3839	-0.2234	-0.2689	0.4036	0.2263	0.7534	-0.0011	-0.1021	0.758	-0.0458	0.5094	111.0829	52.2019	50.3878
17	5.8078	2.9798	-0.8524	8.5341	2.0078	6.9469	0.4737	-0.3922	1.5006	0.9512	0.0402	0.2966	-1.0051	-1.9015	-0.4738	0.6885	0.1529	0.1785	0.8647	-0.0729	0.7699	98.8869	54.0433	51.9691

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 42 through 125 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 126 through 196 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 197 through 270 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 42 through 118 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 119 through 229 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 230 through 270 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 43 through 88 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 89 through 125 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 126 through 214 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 215 through 269 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 43 through 67 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 68 through 118 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 119 through 141 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 142 through 186 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 187 through 220 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 221 through 253 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 254 through 269 )

-
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://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