PDB-5hx0: Crystal structure of unknown function protein Dfer_1899 fromDyado...

ID or keywords:

Entry

Database: PDB / ID: 5hx0

Title

Crystal structure of unknown function protein Dfer_1899 fromDyadobacter fermentans DSM 18053

Components

Uncharacterized protein Dfer_1899

Keywords

Structural Genomics / Unknown Function / Midwest Center for Structural Genomics / MCSG / PSI-Biology

Function / homology

Function and homology information

exo-alpha-sialidase activity
Similarity search - Function

Biological species

Dyadobacter fermentans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.851 Å

Authors

Chang, C. / Duke, N. / Clancy, S. / Chhor, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of unknown function protein Dfer_1899 fromDyadobacter fermentans DSM 18053
Authors: Chang, C. / Duke, N. / Clancy, S. / Chhor, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Jan 29, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 17, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hx0.cif.gz	310.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5hx0.ent.gz	261.1 KB	Display	PDB format
PDBx/mmJSON format	5hx0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5hx0_validation.pdf.gz	468.1 KB	Display	wwPDB validaton report
Full document	5hx0_full_validation.pdf.gz	471.1 KB	Display
Data in XML	5hx0_validation.xml.gz	35.6 KB	Display
Data in CIF	5hx0_validation.cif.gz	53.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hx/5hx0 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/5hx0	HTTPS FTP

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Related structure data

Similar structure data	5igp-2 1ir3-1 4xiy-1 5yu1-1 5d8z-d 5mj7-d 6l2i-d 3cas-d 4qqs-d 4mjz-d 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: MCSG-APC103440

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#113 - May 2009 Influenza Neuraminidase similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (1)

Deposited unit

A: Uncharacterized protein Dfer_1899

B: Uncharacterized protein Dfer_1899

hetero molecules

90.5 kDa, 2 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)	54.698, 85.441, 158.812
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Uncharacterized protein Dfer_1899 Mass: 44752.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / NS114) (bacteria) Strain: ATCC 700827 / DSM 18053 / NS114 / Gene: Dfer_1899 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C6VW01

#1: Protein

Uncharacterized protein Dfer_1899

Mass: 44752.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / NS114) (bacteria)
Strain: ATCC 700827 / DSM 18053 / NS114 / Gene: Dfer_1899 / Plasmid: pMCSG57 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C6VW01

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Non-polymers , 5 types, 783 molecules

#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.09 Å³/Da / Density % sol: 41.1 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.17 M Ammonium sulfate, 0.085M Sodium Acetate, 25.5 % PEG4000, 15 % Glycerol

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.9792915 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 8, 2012

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792915 Å / Relative weight: 1

Reflection

Resolution: 1.85→50 Å / Num. obs: 64380 / % possible obs: 100 % / Redundancy: 8.8 % / B_iso Wilson estimate: 18.22 Å² / R_merge(I) obs: 0.073 / R_pim(I) all: 0.026 / R_rim(I) all: 0.078 / Χ²: 0.904 / Net I/av σ(I): 31.043 / Net I/σ(I): 10.8 / Num. measured all: 566421

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.85-1.88	7.5	0.899	3162	0.83	0.344	0.966	0.815	99.7
1.88-1.92	8	0.755	3146	0.869	0.281	0.807	0.843	100
1.92-1.95	8.6	0.704	3210	0.891	0.253	0.749	0.869	100
1.95-1.99	8.8	0.554	3136	0.931	0.197	0.589	0.864	100
1.99-2.04	9	0.462	3200	0.955	0.162	0.49	0.886	100
2.04-2.08	9	0.397	3172	0.967	0.139	0.422	0.895	100
2.08-2.14	9	0.335	3173	0.973	0.117	0.355	0.902	100
2.14-2.19	9.1	0.285	3217	0.979	0.099	0.302	0.924	100
2.19-2.26	9.1	0.235	3164	0.985	0.082	0.249	0.904	100
2.26-2.33	9	0.193	3165	0.99	0.068	0.204	0.909	100
2.33-2.41	9	0.182	3226	0.99	0.064	0.193	0.909	100
2.41-2.51	9.1	0.145	3215	0.994	0.051	0.154	0.929	100
2.51-2.63	9.1	0.117	3205	0.995	0.041	0.124	0.91	100
2.63-2.76	9	0.091	3219	0.995	0.032	0.096	0.893	100
2.76-2.94	9	0.07	3219	0.997	0.024	0.074	0.88	100
2.94-3.16	9	0.05	3246	0.998	0.018	0.053	0.875	100
3.16-3.48	9	0.035	3242	0.999	0.012	0.037	0.82	100
3.48-3.99	8.9	0.028	3263	0.999	0.01	0.03	0.78	100
3.99-5.02	8.8	0.024	3325	0.999	0.008	0.025	0.744	100
5.02-50	8.1	0.038	3475	0.997	0.014	0.041	1.534	99.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.2	data extraction
HKL-3000		data reduction
HKL-3000		phasing
SBC-Collect		data collection
ARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.851→39.847 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.64 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.1944	5525	4.98 %
R_work	0.1544	-	-
obs	0.1564	62028	90.48 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.851→39.847 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5681	0	69	773	6523

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5965
X-RAY DIFFRACTION	f_angle_d	0.981	8091
X-RAY DIFFRACTION	f_dihedral_angle_d	13.821	3528
X-RAY DIFFRACTION	f_chiral_restr	0.063	849
X-RAY DIFFRACTION	f_plane_restr	0.006	1056

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 (%)
1.8505-1.8716	0.2912	77	0.2287	1833	X-RAY DIFFRACTION	47
1.8716-1.8936	0.2478	96	0.2168	2035	X-RAY DIFFRACTION	52
1.8936-1.9167	0.2564	108	0.1964	2266	X-RAY DIFFRACTION	59
1.9167-1.9409	0.2469	122	0.1957	2570	X-RAY DIFFRACTION	65
1.9409-1.9665	0.2005	150	0.1912	2774	X-RAY DIFFRACTION	72
1.9665-1.9934	0.2465	171	0.179	3008	X-RAY DIFFRACTION	78
1.9934-2.0219	0.2171	163	0.1721	3249	X-RAY DIFFRACTION	83
2.0219-2.0521	0.2218	170	0.1808	3297	X-RAY DIFFRACTION	86
2.0521-2.0841	0.2138	182	0.1832	3525	X-RAY DIFFRACTION	90
2.0841-2.1183	0.201	211	0.1868	3607	X-RAY DIFFRACTION	93
2.1183-2.1548	0.2194	184	0.1783	3709	X-RAY DIFFRACTION	95
2.1548-2.194	0.2255	180	0.178	3816	X-RAY DIFFRACTION	97
2.194-2.2362	0.2316	215	0.1725	3778	X-RAY DIFFRACTION	99
2.2362-2.2818	0.2382	162	0.1709	3949	X-RAY DIFFRACTION	100
2.2818-2.3315	0.2086	213	0.1597	3792	X-RAY DIFFRACTION	100
2.3315-2.3857	0.2104	199	0.1642	3951	X-RAY DIFFRACTION	100
2.3857-2.4453	0.2135	210	0.1558	3842	X-RAY DIFFRACTION	100
2.4453-2.5114	0.175	203	0.1598	3917	X-RAY DIFFRACTION	100
2.5114-2.5853	0.2121	185	0.1655	3875	X-RAY DIFFRACTION	100
2.5853-2.6688	0.2456	232	0.1556	3873	X-RAY DIFFRACTION	100
2.6688-2.7641	0.2264	181	0.1506	3898	X-RAY DIFFRACTION	100
2.7641-2.8748	0.2046	241	0.1539	3847	X-RAY DIFFRACTION	100
2.8748-3.0056	0.1804	218	0.1541	3873	X-RAY DIFFRACTION	100
3.0056-3.164	0.1904	211	0.1597	3875	X-RAY DIFFRACTION	100
3.164-3.3621	0.2065	174	0.1508	3907	X-RAY DIFFRACTION	100
3.3621-3.6215	0.1843	246	0.1434	3833	X-RAY DIFFRACTION	100
3.6215-3.9857	0.2001	210	0.1343	3861	X-RAY DIFFRACTION	100
3.9857-4.5617	0.1363	221	0.1196	3885	X-RAY DIFFRACTION	100
4.5617-5.7445	0.1337	169	0.1203	3902	X-RAY DIFFRACTION	100
5.7445-39.8559	0.1762	221	0.1586	3863	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	0.0575	-0.0493	-0.0296	0.0667	0.0295	0.4763	-0.0602	-0.0252	-0.0411	0.0353	-0.0358	-0.0872	-0.1996	-0.0096	-0.038	-0.0127	0.0046	-0.0193	0.059	0.0275	0.0918	33.722	79.037	-6.9781
2	0.0226	0.0064	0.039	0.0231	0.0071	0.0658	0.0041	0.0054	0.0173	-0.0315	-0.0299	0.0465	-0.1095	-0.1146	-0.0272	0.1548	0.0894	-0.0374	0.0942	-0.0115	0.1081	21.6653	91.4332	-6.5953
3	0.037	0.0437	-0.0108	0.1444	-0.0875	0.0971	0.0256	-0.0081	0.026	0.1412	-0.0312	0.0663	-0.2445	-0.1395	-0.0026	0.1812	0.0503	-0.0161	0.123	-0.0315	0.1221	22.4233	91.6408	6.6538
4	0.0685	-0.0371	-0.0167	0.1452	0.0607	0.106	-0.0993	-0.0979	0.0214	0.2312	-0.0268	-0.0723	-0.0191	0.0564	-0.1452	0.1237	-0.0108	-0.0375	0.0988	0.0113	0.0815	33.5297	76.8049	12.2307
5	0.0505	0.0484	-0.0556	0.0517	-0.0586	0.0667	-0.1366	0.1106	-0.068	-0.1078	-0.047	0.0453	0.0121	-0.172	-0.0244	0.13	0.0194	-0.0291	0.2558	-0.0797	0.125	28.3986	77.9028	-40.4731
6	0.217	-0.0415	-0.0266	0.2514	0.0404	0.4396	-0.1355	0.0547	-0.0879	-0.0817	-0.1011	-0.1031	0.045	-0.1875	-0.2847	0.0518	-0.07	0.0619	0.0973	0.0189	0.1089	38.7247	76.4452	-26.8745
7	0.0535	-0.0126	0.0004	0.016	-0.0023	0.0037	-0.0779	-0.039	-0.0324	-0.049	-0.0145	-0.0496	0.2176	0.1017	-0.0057	0.1733	0.0167	0.0622	0.1273	0.0476	0.1816	51.8268	68.7012	-30.2118
8	0.0252	-0.0135	-0.0043	0.0121	-0.0031	0.0458	-0.072	-0.0107	-0.1223	-0.0595	-0.037	-0.0626	0.1191	0.1111	-0.0181	0.2163	-0.0161	0.1723	0.0466	0.1116	0.1748	52.8738	69.6333	-40.5771
9	0.3131	0.0868	-0.0922	0.3793	0.2241	0.675	-0.1893	0.0848	-0.1399	-0.2706	-0.088	-0.0404	0.0425	-0.3157	-0.2975	0.2284	-0.0287	0.0374	0.1467	-0.0301	0.0887	38.4424	73.7385	-49.0214

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 35 through 182 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 183 through 216 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 217 through 315 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 316 through 399 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 36 through 62 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 63 through 182 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 183 through 216 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 217 through 286 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 287 through 399 )

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