PDB-4hn9: Crystal structure of iron ABC transporter solute-binding protein ...

ID or keywords:

Entry

Database: PDB / ID: 4hn9

Title

Crystal structure of iron ABC transporter solute-binding protein from Eubacterium eligens

Components

Iron complex transport system substrate-binding protein

Keywords

TRANSPORT PROTEIN /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / transport

Function / homology

Function and homology information

Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2180 / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle /

Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology

Biological species

Eubacterium eligens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Michalska, K. / Mack, J.C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of iron ABC transporter solute-binding protein from Eubacterium eligens
Authors: Michalska, K. / Mack, J.C. / Endres, M. / Joachimiak, A.

History

Deposition	Oct 19, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 12, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hn9.cif.gz	249 KB	Display	PDBx/mmCIF format
PDB format	pdb4hn9.ent.gz	210.5 KB	Display	PDB format
PDBx/mmJSON format	4hn9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hn/4hn9 ftp://data.pdbj.org/pub/pdb/validation_reports/hn/4hn9	HTTPS FTP

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Related structure data

Similar structure data	5aho-d 5t1p-5 1r1w-d 4eqa-2 6iyw-3 4fqb-1 5t3q-d 1glv-d 6euv-1 3ckm-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 - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC110562

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Iron complex transport system substrate-binding protein

B: Iron complex transport system substrate-binding protein

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

1

A: Iron complex transport system substrate-binding protein

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

2

B: Iron complex transport system substrate-binding protein

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

Unit cell

Length a, b, c (Å)	61.870, 57.564, 79.299
Angle α, β, γ (deg.)	90.00, 98.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

#1: Protein	Iron complex transport system substrate-binding protein Mass: 36042.727 Da / Num. of mol.: 2 / Fragment: UNP residues 24-355 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium eligens (bacteria) / Strain: ATCC 27750 / Gene: EUBELI_01498, FepB / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: C4Z2B5
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Iron complex transport system substrate-binding protein

Mass: 36042.727 Da / Num. of mol.: 2 / Fragment: UNP residues 24-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Eubacterium eligens (bacteria) / Strain: ATCC 27750 / Gene: EUBELI_01498, FepB / Plasmid: pMCSG68 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: C4Z2B5

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 280 / 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: 1.94 Å³/Da / Density % sol: 36.56 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 35% PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2012 / Details: mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97923 Å / Relative weight: 1
Reflection	Resolution: 1.85→30 Å / Num. all: 47314 / Num. obs: 47253 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / B_iso Wilson estimate: 22.9 Å² / R_merge(I) obs: 0.084 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.724 / Mean I/σ(I) obs: 1.98 / Num. unique all: 2354 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHENIX		model building
SHELXD		phasing
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.85→30.012 Å / SU ML: 0.17 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.83 / Stereochemistry target values: ML / Details: HYDROGEN ATOMS HAVE BEEN ADDED AT RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1982	1212	2.57 %	random
R_work	0.1496	-	-	-
all	0.1509	47227	-	-
obs	0.1509	47227	99.78 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→30.012 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4826	0	0	280	5106

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	4932
X-RAY DIFFRACTION	f_angle_d	1.395	6735
X-RAY DIFFRACTION	f_dihedral_angle_d	13.103	1753
X-RAY DIFFRACTION	f_chiral_restr	0.087	807
X-RAY DIFFRACTION	f_plane_restr	0.007	864

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 (%)
1.85-1.9241	0.218	133	0.1918	5091	X-RAY DIFFRACTION	99
1.9241-2.0116	0.2417	133	0.1839	5027	X-RAY DIFFRACTION	100
2.0116-2.1177	0.2375	124	0.1698	5133	X-RAY DIFFRACTION	100
2.1177-2.2503	0.2503	135	0.1623	5079	X-RAY DIFFRACTION	100
2.2503-2.424	0.1987	144	0.1546	5102	X-RAY DIFFRACTION	100
2.424-2.6678	0.2178	133	0.1532	5113	X-RAY DIFFRACTION	100
2.6678-3.0535	0.2251	140	0.1554	5125	X-RAY DIFFRACTION	100
3.0535-3.8458	0.1732	143	0.1394	5143	X-RAY DIFFRACTION	100
3.8458-30.0157	0.1625	127	0.1322	5202	X-RAY DIFFRACTION	99

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	0.7135	0.8001	-0.3466	0.8631	-0.4012	0.1684	-0.2038	0.2685	-0.1359	-0.3946	0.2545	-0.1088	0.0674	-0.0035	0.0005	0.2297	-0.0296	-0.0026	0.2093	-0.0019	0.2424	46.9117	15.5895	54.8917
2	0.7523	-0.0061	0.6185	2.2966	-0.2154	0.919	0.0158	-0.0899	0.1129	0.1604	0.0158	-0.0361	0.0077	-0.0229	0	0.1297	-0.0066	-0.0109	0.1428	0.0003	0.1882	46.7331	12.97	73.7702
3	0.4751	-0.0592	0.15	0.6742	-0.438	1.0895	-0.0377	-0.053	0.0184	-0.0987	0.0077	0.142	-0.1008	-0.1498	0	0.1536	-0.0068	0.0059	0.1311	-0.0015	0.1696	42.5981	21.8598	65.029
4	0.5323	0.2208	-0.0801	0.2083	0.0713	0.1724	0.0437	0.1887	0.086	-0.2279	0.0463	0.1013	-0.1567	-0.1276	0.0052	0.1997	-0.0078	0.004	0.1631	0.0033	0.1304	33.2982	6.2195	53.2559
5	0.9709	-0.2468	-0.3415	1.0869	-0.6224	0.6091	0.0163	0.1609	0.1421	0.0671	-0.0613	-0.0457	-0.1066	-0.0157	0.0001	0.1713	0.0175	-0.0179	0.1832	0.0119	0.1856	16.5349	9.7353	68.3546
6	0.2281	-0.0803	-0.0006	0.8273	0.2816	0.4673	0.0186	-0.0396	0.154	0.0257	-0.0639	-0.0148	-0.1667	-0.1799	0	0.1856	0.0342	-0.0139	0.2062	0.0083	0.2092	13.6185	11.9169	69.5265
7	0.2268	-0.1058	-0.061	1.1722	0.1183	1.5368	0.1057	-0.3683	-0.192	0.2681	-0.1536	0.1204	0.053	-0.0636	-0.0001	0.1704	-0.0079	0.0137	0.1748	0.0137	0.1722	17.1195	0.5462	75.7297
8	1.3807	0.2251	-0.252	0.3119	-0.1939	0.9167	-0.0628	-0.0214	-0.2055	0.0478	0.0428	0.0064	0.0815	-0.074	0	0.119	-0.0058	-0.0017	0.0964	-0.0152	0.1365	29.8528	-1.07	62.2271
9	0.2201	0.2576	-0.0305	0.4151	-0.1772	0.1458	-0.1782	-0.5302	-0.234	0.2841	0.2594	-0.0786	0.0623	0.0348	-0.0016	0.3188	0.0617	0.0324	0.3177	0.0387	0.3294	1.9968	30.507	69.5636
10	0.7068	0.003	0.2124	2.3422	0.3981	1.082	0.0224	0.1785	0.081	-0.3049	0.0072	0.0426	-0.0139	-0.057	-0.0001	0.1606	0.0271	-0.0083	0.1719	-0.001	0.1594	-3.1804	42.2903	46.7154
11	1.1255	0.2289	-0.3368	1.0314	0.6525	1.4858	0.125	0.1405	0.2069	-0.1116	-0.0334	-0.0992	-0.3199	0.0502	0.0074	0.1691	0.0303	0.013	0.127	0.0175	0.1744	0.4876	49.0053	53.3143
12	0.3894	-0.1442	-0.1457	0.3193	-0.0795	0.3583	-0.0627	-0.406	-0.1268	0.0659	0.0202	-0.0165	-0.1542	0.0892	0.0017	0.168	0.0147	0.0059	0.1718	0.0084	0.1249	12.1549	33.8762	65.4853
13	1.0207	0.3153	-0.2647	0.9559	0.3604	0.3073	-0.0573	-0.1244	0.1354	-0.0579	-0.1125	-0.011	-0.1888	0.1989	0.0007	0.1596	0.0073	-0.0122	0.2162	-0.0069	0.1428	28.7855	38.5208	49.4377
14	0.146	-0.107	-0.1728	0.2953	0.06	0.2228	-0.1504	-0.1901	0.297	0.0932	0.048	0.0987	-0.1735	0.0831	-0.0004	0.228	0.035	-0.0124	0.2237	0.0171	0.2253	23.5755	39.8539	56.0765
15	1.5274	0.5733	-0.1961	1.4613	-0.3347	2.4113	0.02	0.1222	-0.0741	-0.2091	-0.0805	-0.1908	0.0559	0.3571	-0.0002	0.1567	0.03	0.0018	0.2324	-0.0141	0.137	30.8359	34.9502	44.8492
16	1.0685	-0.0316	-0.2716	0.3473	-0.2239	0.6718	0.0206	0.0832	-0.1336	-0.0054	-0.0674	-0.0243	0.1016	0.1447	0	0.1387	0.041	-0.0033	0.1276	-0.0008	0.1373	14.2296	27.3869	56.2011

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 39:72)
2	X-RAY DIFFRACTION	2	(chain A and resid 73:142)
3	X-RAY DIFFRACTION	3	(chain A and resid 143:184)
4	X-RAY DIFFRACTION	4	(chain A and resid 185:205)
5	X-RAY DIFFRACTION	5	(chain A and resid 206:231)
6	X-RAY DIFFRACTION	6	(chain A and resid 232:268)
7	X-RAY DIFFRACTION	7	(chain A and resid 269:308)
8	X-RAY DIFFRACTION	8	(chain A and resid 309:354)
9	X-RAY DIFFRACTION	9	(chain B and resid 32:55)
10	X-RAY DIFFRACTION	10	(chain B and resid 56:141)
11	X-RAY DIFFRACTION	11	(chain B and resid 142:186)
12	X-RAY DIFFRACTION	12	(chain B and resid 187:207)
13	X-RAY DIFFRACTION	13	(chain B and resid 208:229)
14	X-RAY DIFFRACTION	14	(chain B and resid 230:242)
15	X-RAY DIFFRACTION	15	(chain B and resid 243:305)
16	X-RAY DIFFRACTION	16	(chain B and resid 306:354)

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