PDB-4j8l: CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT protein...

ID or keywords:

Entry

Database: PDB / ID: 4j8l

Title

CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT protein YhfS from Escherichia coli

Components

Uncharacterized protein YhfS

Keywords

UNKNOWN FUNCTION / Two domains / PLP covalently attached to Lysine

Function / homology

Function and homology information

biosynthetic process / catalytic activity / pyridoxal phosphate binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.651 Å

Authors

Fedorov, A.A. / Fedorov, E.V. / Xiang, D.F. / Raushel, F.M. / Almo, S.C.

Citation

Journal: To be Published
Title: Crystal structure of the pyridoxal-5'-phosphate dependent protein yhfs from escherichia coli
Authors: Fedorov, A.A. / Fedorov, E.V. / Xiang, D.F. / Raushel, F.M. / Almo, S.C.

History

Deposition	Feb 14, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 5, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4j8l.cif.gz	149.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4j8l.ent.gz	125.2 KB	Display	PDB format
PDBx/mmJSON format	4j8l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4j8l_validation.pdf.gz	435.4 KB	Display	wwPDB validaton report
Full document	4j8l_full_validation.pdf.gz	435.7 KB	Display
Data in XML	4j8l_validation.xml.gz	17.5 KB	Display
Data in CIF	4j8l_validation.cif.gz	26 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j8/4j8l ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j8l	HTTPS FTP

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Related structure data

Similar structure data	7c6r-d 6r1b-3 3dtw-1 3u6j-d 5t4k-d 3ke3-d 6a8z-2 7c6x-4 4hn9-2 3q2q-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Uncharacterized protein YhfS

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: Uncharacterized protein YhfS

hetero molecules

A: Uncharacterized protein YhfS

hetero molecules

defined by author&software
78.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.915, 134.915, 75.142
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	180
Space group name H-M	P6₂22

Components on special symmetry positions

ID	Model	Components
1	1	A-512- HOH
2	1	A-752- HOH
3	1	A-756- HOH
4	1	A-758- HOH

#1: Protein	Uncharacterized protein YhfS Mass: 39052.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yhfS, b3376, JW3339 / Production host: Escherichia coli (E. coli) / References: UniProt: P45545
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.53 Å³/Da / Density % sol: 51.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.4M sodium acetate, 0.1M sodium cacodylate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2013
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.651→46.121 Å / Num. all: 48578 / Num. obs: 48578 / % possible obs: 99.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
CBASS		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.651→46.121 Å / SU ML: 0.16 / σ(F): 1 / Phase error: 21.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1952	2454	5.05 %	RANDOM
R_work	0.1691	-	-	-
obs	0.1705	48578	99.78 %	-
all	-	48578	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.651→46.121 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2732	0	20	276	3028

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2820
X-RAY DIFFRACTION	f_angle_d	1.068	3836
X-RAY DIFFRACTION	f_dihedral_angle_d	13.062	1043
X-RAY DIFFRACTION	f_chiral_restr	0.069	447
X-RAY DIFFRACTION	f_plane_restr	0.006	510

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 (%)
1.6514-1.6832	0.286	115	0.2272	2499	X-RAY DIFFRACTION	98
1.6832-1.7175	0.2312	132	0.2061	2512	X-RAY DIFFRACTION	100
1.7175-1.7549	0.235	124	0.1905	2542	X-RAY DIFFRACTION	100
1.7549-1.7957	0.2461	150	0.1995	2506	X-RAY DIFFRACTION	100
1.7957-1.8406	0.2362	117	0.1859	2543	X-RAY DIFFRACTION	100
1.8406-1.8904	0.2171	138	0.1767	2518	X-RAY DIFFRACTION	100
1.8904-1.946	0.2378	147	0.1711	2518	X-RAY DIFFRACTION	100
1.946-2.0088	0.2043	150	0.1732	2520	X-RAY DIFFRACTION	100
2.0088-2.0806	0.2005	141	0.1643	2547	X-RAY DIFFRACTION	100
2.0806-2.1639	0.2121	119	0.1677	2549	X-RAY DIFFRACTION	100
2.1639-2.2624	0.2079	126	0.17	2552	X-RAY DIFFRACTION	100
2.2624-2.3817	0.2138	137	0.1694	2559	X-RAY DIFFRACTION	100
2.3817-2.5309	0.2171	132	0.1747	2581	X-RAY DIFFRACTION	100
2.5309-2.7263	0.1753	135	0.1793	2569	X-RAY DIFFRACTION	100
2.7263-3.0006	0.2108	145	0.1854	2586	X-RAY DIFFRACTION	100
3.0006-3.4346	0.1958	158	0.1776	2589	X-RAY DIFFRACTION	100
3.4346-4.3268	0.1565	147	0.1476	2630	X-RAY DIFFRACTION	100
4.3268-46.139	0.1797	141	0.1552	2804	X-RAY DIFFRACTION	100

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	2.1218	-2.1999	-1.8242	7.4331	2.8857	3.4447	0.0738	0.2711	-0.174	-0.6479	-0.1527	0.1524	-0.1035	-0.0576	0.0539	0.1583	-0.019	-0.0448	0.1657	-0.0065	0.1365	25.2805	51.2025	36.403
2	0.6951	1.3472	-1.9082	2.7456	-4.0002	5.8913	0.0996	-0.0774	0.1546	0.1865	-0.014	0.24	-0.2493	-0.0003	-0.1049	0.1344	-0.0029	0.0293	0.1635	-0.0071	0.1992	15.8308	61.4237	60.3316
3	2.3812	0.9923	2.1702	0.973	0.1028	7.473	0.0266	-0.0485	0.0975	-0.0938	-0.015	0.2989	-0.3415	-0.2448	0.0022	0.0902	0.0128	0.0165	0.1142	0.0103	0.1689	14.6742	53.1325	52.2987
4	1.1066	-0.4885	-0.144	1.7535	-0.0704	1.7453	-0.0391	0.1658	-0.3512	-0.2137	0.0031	0.14	0.4001	-0.223	-0.02	0.2569	-0.0719	-0.0155	0.1719	-0.0688	0.2808	17.6892	29.1714	45.7156
5	0.7893	-0.053	-0.4576	0.9788	0.2325	2.0115	0.0288	0.069	-0.0314	-0.0534	0.0239	0.159	0.103	-0.1236	-0.0504	0.1519	-0.0089	-0.0081	0.1368	-0.0098	0.2081	19.3338	44.9573	51.3608
6	4.8586	-0.9281	-5.3143	0.8516	0.9467	6.3122	0.11	-0.0376	0.1541	-0.1855	0.0816	0.0666	-0.1408	0.2009	-0.2062	0.1439	-0.0003	-0.01	0.1196	-0.0109	0.1222	33.4635	51.8143	41.7231
7	2.3673	-0.646	-0.1828	1.5425	0.4373	2.0001	0.0014	0.1916	-0.3196	-0.1261	-0.039	-0.1255	0.1164	0.094	0.0194	0.1912	0.0226	0.0624	0.1225	-0.0079	0.2041	47.9494	35.6855	37.8333
8	1.7673	-0.2685	-0.1595	4.0974	1.9714	2.2116	-0.0183	-0.0018	-0.2769	0.217	-0.0433	0.0361	0.3024	-0.0254	0.0777	0.1451	0.0083	0.0236	0.1324	-0.0058	0.1773	42.6044	37.1608	47.0511
9	5.0566	0.7016	-1.0558	4.2027	0.1401	1.5383	-0.0579	-0.0305	0.0336	-0.3261	0.0499	-0.2878	-0.0318	0.1012	0.0045	0.2142	0.0168	0.0445	0.1362	-0.0235	0.1069	49.3324	44.3903	39.1797

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 49 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 73 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 74 through 170 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 171 through 228 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 229 through 261 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 262 through 299 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 300 through 336 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 337 through 361 )

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