PDB-4pf6: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR...

ID or keywords:

Entry

Database: PDB / ID: 4pf6

Title

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS (RD1_0742, TARGET EFI-510239) WITH BOUND 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID (KDO)

Components

C4-dicarboxylate-binding protein

Keywords

TRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

transmembrane transport / periplasmic space
Similarity search - Function

Biological species

Roseobacter denitrificans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...

History

Deposition	Apr 28, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 25, 2015	Group: Database references
Revision 1.2	Oct 7, 2015	Group: Experimental preparation
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Refinement description Category: pdbx_audit_support / pdbx_struct_oper_list / software Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	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
Revision 1.6	Dec 27, 2023	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4pf6.cif.gz	195.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4pf6_validation.pdf.gz	455.4 KB	Display	wwPDB validaton report
Full document	4pf6_full_validation.pdf.gz	456.5 KB	Display
Data in XML	4pf6_validation.xml.gz	17.5 KB	Display
Data in CIF	4pf6_validation.cif.gz	27.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pf/4pf6 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/4pf6	HTTPS FTP

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Related structure data

Related structure data	4ln5C 4mcoC 4mevC 4mhfC 4mijC 4mncC 4mniC 4mx6C 4n15C 4n17C 4n4uC 4n6dC 4n6kC 4n8gC 4n8yC 4n91C 4napC 4nf0C 4ng7C 4nguC 4nhbC 4nn3C 4nq8C 4nx1C 4o7mC 4o8mC 4o94C 4oa4C 4oanC 4ovpC 4ovqC 4ovrC 4ovsC 4ovtC 4p1eC 4p1lC 4p3lC 4p47C 4p56C 4p8bC 4p9kC 4pafC 4paiC 4pakC 4pbhC 4pbqC 4pc9C 4pcdC 4pddC 4pdhC 4pe3C 4petC 4pf8C 4pfbC 4pfiC 4pfrC 4pgnC 4pgpC 4uabC C: citing same article (ref.)
Similar structure data	6obb-d 6op9-d 6vzn-1 4xeq-4 4oa4-4 4ovq-d 5eol-d 3gen-d 3peq-1 2vpn-1 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: EFI-510239

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: C4-dicarboxylate-binding protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	100.527, 100.527, 159.213
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-613- HOH

Details

biological unit is a monomer

#1: Protein

C4-dicarboxylate-binding protein / TRAP PERIPLASMIC SOLUTE BINDING PROTEIN

Mass: 36671.328 Da / Num. of mol.: 1 / Fragment: UNP residues 25-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Roseobacter denitrificans (bacteria) / Strain: ATCC 33942 / OCh 114 / Gene: RD1_0742 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16C67

#2: Sugar

ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid

Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₄O₈

#3: Chemical

ChemComp-PGE / TRIETHYLENE GLYCOL

Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄

#4: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H₂O

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: 3.17 Å³/Da / Density % sol: 61.15 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein (31.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.2 M Sodium Chloride, 0.1 M Sodium Cacodylate pH 6.5, 2 M Ammonium Sulfate ); Cryoprotection (80% LiSO4 (2 M) + 20% reservoir

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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: Apr 9, 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: 1.7→159.21 Å / Num. obs: 52900 / % possible obs: 100 % / Redundancy: 20.3 % / B_iso Wilson estimate: 19.52 Å² / R_merge(I) obs: 0.104 / R_pim(I) all: 0.023 / Net I/σ(I): 25 / Num. measured all: 1071804 / Scaling rejects: 27

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	% possible all
1.7-1.73	18.9	0.01078	3.5	51916	2750	0.254	100
9-159.21	15.1	0.045	66.1	6870	454	0.011	99.1

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.1_1168)	refinement
PDB_EXTRACT	3.14	data extraction
Aimless		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.75→47.93 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.162	2453	5.09 %	Random Selection
R_work	0.139	-	-	-
obs	0.14	48520	99.9 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 23.04 Å²

Refinement step

Cycle: final / Resolution: 1.75→47.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2347	0	63	434	2844
B_iso mean	-	-	31.14	35.08	-
Num. residues	-	-	-	-	305

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2475
X-RAY DIFFRACTION	f_angle_d	1.127	3379
X-RAY DIFFRACTION	f_dihedral_angle_d	14.952	888
X-RAY DIFFRACTION	f_chiral_restr	0.066	381
X-RAY DIFFRACTION	f_plane_restr	0.006	448

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 (%)
1.7501-1.77	0.2078	162	0.1969	2857	X-RAY DIFFRACTION	100
1.77-1.7908	0.2212	135	0.1943	2919	X-RAY DIFFRACTION	100
1.7908-1.8126	0.2271	157	0.1833	2873	X-RAY DIFFRACTION	100
1.8126-1.8356	0.2188	155	0.1715	2869	X-RAY DIFFRACTION	100
1.8356-1.8597	0.1852	160	0.1667	2860	X-RAY DIFFRACTION	100
1.8597-1.8852	0.1958	169	0.1596	2851	X-RAY DIFFRACTION	100
1.8852-1.9122	0.2094	146	0.1514	2878	X-RAY DIFFRACTION	100
1.9122-1.9407	0.2108	137	0.1498	2904	X-RAY DIFFRACTION	100
1.9407-1.971	0.1727	153	0.1455	2849	X-RAY DIFFRACTION	100
1.971-2.0033	0.1904	109	0.1452	2922	X-RAY DIFFRACTION	100
2.0033-2.0379	0.1378	168	0.1301	2856	X-RAY DIFFRACTION	100
2.0379-2.0749	0.1389	145	0.129	2861	X-RAY DIFFRACTION	100
2.0749-2.1148	0.142	185	0.1211	2829	X-RAY DIFFRACTION	100
2.1148-2.158	0.1493	141	0.118	2885	X-RAY DIFFRACTION	100
2.158-2.2049	0.1492	141	0.1218	2899	X-RAY DIFFRACTION	100
2.2049-2.2562	0.1687	146	0.1252	2875	X-RAY DIFFRACTION	100
2.2562-2.3126	0.1665	174	0.1236	2871	X-RAY DIFFRACTION	100
2.3126-2.3752	0.1454	181	0.1154	2827	X-RAY DIFFRACTION	100
2.3752-2.4451	0.1419	144	0.122	2890	X-RAY DIFFRACTION	100
2.4451-2.524	0.146	133	0.1167	2882	X-RAY DIFFRACTION	100
2.524-2.6142	0.1445	169	0.1221	2846	X-RAY DIFFRACTION	100
2.6142-2.7188	0.157	170	0.1363	2887	X-RAY DIFFRACTION	100
2.7188-2.8426	0.1693	144	0.1408	2874	X-RAY DIFFRACTION	100
2.8426-2.9924	0.1759	141	0.1441	2880	X-RAY DIFFRACTION	100
2.9924-3.1799	0.1758	164	0.1564	2859	X-RAY DIFFRACTION	100
3.1799-3.4253	0.1597	130	0.1452	2895	X-RAY DIFFRACTION	100
3.4253-3.7699	0.1692	157	0.1325	2873	X-RAY DIFFRACTION	100
3.7699-4.3151	0.1413	163	0.1239	2858	X-RAY DIFFRACTION	100
4.3151-5.4354	0.133	168	0.1276	2854	X-RAY DIFFRACTION	100
5.4354-47.9496	0.1792	171	0.1705	2841	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	1.5105	-0.2439	-0.1048	1.027	-0.3084	1.4156	0.0053	-0.1324	0.0605	0.1815	0.0042	0.0848	-0.2009	-0.1839	0.0133	0.1786	0.0082	0.0462	0.1221	-0.0232	0.146	28.5326	11.8962	-8.3402
2	0.4561	-0.1779	0.0205	0.627	-0.0205	1.0896	0.0148	0.0239	0.0847	-0.0123	0.0569	-0.0979	-0.1694	0.0817	-0.0644	0.1725	-0.0211	0.0403	0.1259	-0.0358	0.1789	39.1222	12.9539	-15.7768
3	0.878	-0.4329	-0.241	0.9021	-0.1958	1.4366	-0.0218	-0.1011	0.0277	0.1406	0.043	-0.1277	0.1241	0.2451	-0.0449	0.1561	0.0119	0.0109	0.1495	-0.0339	0.1595	43.2601	3.3636	-14.899
4	1.0885	-0.2022	-0.3664	1.7404	0.4278	1.209	0.0221	0.1742	0	-0.3711	-0.0601	0.1283	-0.1916	-0.2248	0.0122	0.1843	-0.0038	0.0003	0.1717	-0.0104	0.1468	32.4914	2.8981	-40.8626
5	0.9905	-0.6467	-0.081	2.2614	0.7518	1.6877	0.0656	0.0988	0.1015	-0.3037	0.0401	-0.2576	-0.3387	0.1179	-0.0883	0.1957	-0.0319	0.0458	0.1365	-0.0061	0.1661	40.5177	9.3139	-34.5881
6	0.3143	-0.0264	-0.2032	0.6658	0.5285	1.4872	0.0074	0.0521	0.0544	-0.0022	-0.0253	0.0331	-0.1374	-0.1469	0.0194	0.1509	0.002	0.0232	0.1266	-0.0138	0.1613	30.8209	7.932	-24.4325
7	1.9782	0.8493	1.8378	1.4001	1.2443	4.4709	0.0811	-0.0634	-0.0821	0.2279	-0.05	0.114	0.4362	-0.4057	-0.0436	0.1905	-0.0333	0.0384	0.1541	-0.0028	0.1814	29.3029	-0.2096	-11.9367
8	2.6037	0.1678	-0.1179	0.8129	-0.101	0.854	0.0804	-0.0705	-0.0619	-0.0054	-0.0602	0.0588	0.2722	-0.1292	-0.0124	0.1661	-0.0615	0.0318	0.1766	-0.0449	0.1696	36.5279	-4.8805	-36.1618
9	1.6576	0.976	-0.5917	2.1797	-0.73	2.736	-0.1088	-0.0363	-0.0805	0.118	0.1194	-0.4448	0.0627	0.4356	-0.0058	0.1918	0.0522	0.0436	0.2751	-0.0771	0.2854	54.1228	-0.9218	-23.4362

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 26 THROUGH 54 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 55 THROUGH 111 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 112 THROUGH 152 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 153 THROUGH 177 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 178 THROUGH 195 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 196 THROUGH 253 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 254 THROUGH 288 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 289 THROUGH 309 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 310 THROUGH 330 )

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