PDB-3r0u: Crystal structure of NYSGRC enolase target 200555, a putative dip...

ID or keywords:

Entry

Database: PDB / ID: 3r0u

Title

Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Tartrate and Mg complex

Components

Enzyme of enolase superfamily

Keywords

LYASE / enolase / structural genomics / putative epimerase / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

racemase and epimerase activity, acting on amino acids and derivatives / racemase and epimerase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / peptide metabolic process / magnesium ion binding
Similarity search - Function

Biological species

Francisella philomiragia subsp. philomiragia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.9 Å

Authors

Vetting, M.W. / Hillerich, B. / Seidel, R.D. / Zencheck, W.D. / Toro, R. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / ...

History

Deposition	Mar 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 6, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 22, 2012	Group: Database references
Revision 1.3	Mar 21, 2012	Group: Database references
Revision 1.4	Mar 28, 2012	Group: Database references
Revision 1.5	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3r0u.cif.gz	303.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3r0u.ent.gz	248.9 KB	Display	PDB format
PDBx/mmJSON format	3r0u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3r0u_validation.pdf.gz	479.3 KB	Display	wwPDB validaton report
Full document	3r0u_full_validation.pdf.gz	483 KB	Display
Data in XML	3r0u_validation.xml.gz	39.1 KB	Display
Data in CIF	3r0u_validation.cif.gz	55.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r0/3r0u ftp://data.pdbj.org/pub/pdb/validation_reports/r0/3r0u	HTTPS FTP

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Related structure data

Related structure data	3ijiC 3ijlC 3ijqC 3ik4C 3jvaC 3jw7C 3jzuC 3k1gC 3kumC 3q45C 3q4dC 3r0kC 3r10C 3r11C 3r1zC 3ritC 3ro6C C: citing same article (ref.)
Similar structure data	3r1z-d 3r0k-d 3r11-d 3dfh-4 3ck5-4 3dfh-3 4dye-2 6fpz-2 6fpy-1 2ps2-1 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	TargetDB: NYSGRC-200555

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (2)

Deposited unit

A: Enzyme of enolase superfamily

B: Enzyme of enolase superfamily

hetero molecules

86.1 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)	121.070, 121.070, 149.040
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	Enzyme of enolase superfamily Mass: 42455.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella philomiragia subsp. philomiragia (bacteria) Strain: ATCC 25017 / Gene: Fphi_1647 / Plasmid: CHS30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1R-RIL / References: UniProt: B0TZW0

#1: Protein

Enzyme of enolase superfamily

Mass: 42455.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Francisella philomiragia subsp. philomiragia (bacteria)
Strain: ATCC 25017 / Gene: Fphi_1647 / Plasmid: CHS30 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1R-RIL / References: UniProt: B0TZW0

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Non-polymers , 5 types, 636 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.22 Å³/Da / Density % sol: 61.75 %
Crystal grow	Temperature: 294 K / pH: 5.6 Details: Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.4 M Ammonium sulfate, 100 mM NaCitrate pH 5.6, ...Details: Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.4 M Ammonium sulfate, 100 mM NaCitrate pH 5.6, KNaTartrate, 20% glycerol, 5mM MgSO4, 10 min, vapor diffusion, sitting drop, temperature 294K

Crystal

Density Matthews: 3.22 Å³/Da / Density % sol: 61.75 %

Crystal grow

Temperature: 294 K / pH: 5.6
Details: Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.4 M Ammonium sulfate, 100 mM NaCitrate pH 5.6, ...

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Data collection

Diffraction	Mean temperature: 98 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97905 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Details: Undulator Source
Radiation	Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97905 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. all: 87501 / Num. obs: 87501 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / B_iso Wilson estimate: 22.48 Å² / R_sym value: 0.117 / Net I/σ(I): 13.3
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 12592 / R_sym value: 0.557 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction
MAR345dtb		data collection
MOSFLM		data reduction
SCALEPACK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.9→30.614 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.9021 / SU ML: 0.17 / σ(F): 0 / Phase error: 16.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1947	1996	2.28 %	random
R_work	0.1613	-	-	-
obs	0.1613	87353	99.87 %	-
all	-	87353	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.763 Å² / k_sol: 0.381 e/Å³

Displacement parameters

B_iso max: 91.29 Å² / B_iso mean: 28.7856 Å² / B_iso min: 7.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.3534 Å²	-0 Å²	0 Å²
2-	-	-0.3534 Å²	0 Å²
3-	-	-	0.7068 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→30.614 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5605	0	65	623	6293

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	5773
X-RAY DIFFRACTION	f_angle_d	1.628	7814
X-RAY DIFFRACTION	f_chiral_restr	0.131	922
X-RAY DIFFRACTION	f_plane_restr	0.008	994
X-RAY DIFFRACTION	f_dihedral_angle_d	13.695	2114

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.9475	0.2548	141	0.2112	6009	6150	100
1.9475-2.0002	0.235	140	0.1862	6002	6142	100
2.0002-2.059	0.2055	141	0.17	6027	6168	100
2.059-2.1254	0.1823	142	0.1609	6024	6166	100
2.1254-2.2014	0.1871	141	0.1551	6047	6188	100
2.2014-2.2895	0.2041	141	0.1495	6043	6184	100
2.2895-2.3937	0.1841	140	0.1469	6035	6175	100
2.3937-2.5198	0.208	143	0.1561	6085	6228	100
2.5198-2.6776	0.2135	142	0.1607	6065	6207	100
2.6776-2.8842	0.195	143	0.1675	6100	6243	100
2.8842-3.1742	0.1893	143	0.1635	6118	6261	100
3.1742-3.6328	0.1823	143	0.1496	6164	6307	100
3.6328-4.5745	0.1647	147	0.1418	6220	6367	100
4.5745-30.6183	0.2118	149	0.1821	6418	6567	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	0.3009	0.1539	0.0781	0.2092	0.1424	0.2992	0.0642	-0.2045	0.0267	0.1438	-0.1536	0.0625	0.0907	-0.1805	0.0154	0.183	-0.0395	-0.0319	0.2163	0.0154	0.1769	72.9921	71.973	56.7595
2	0.1899	0.045	0.1085	0.0191	0.0578	0.2702	-0.0097	0.0149	0.114	-0.0296	-0.0179	-0.0202	0.028	0.0196	0.0075	0.0758	-0.0073	-0.0241	0.0883	-0.001	0.0966	82.7524	80.1414	51.2897
3	0.046	0.0252	-0.0209	0.024	0.0116	0.0448	-0.0007	-0.0335	-0.0435	-0.0419	-0.0344	0.0655	0.0367	-0.0674	0.0087	0.1307	-0.0102	-0.0614	0.1544	-0.0479	0.1538	71.0553	72.6023	41.92
4	0.001	-0.0047	0.0118	0.0051	-0.0039	-0.0022	0.0064	-0.0857	-0.1389	0.1037	-0.059	-0.048	0.1191	0.0134	-0.1125	0.3619	-0.2487	-0.401	-0.0107	0.0265	0.4713	81.907	42.4018	55.2167
5	0.0048	-0.0088	-0.0082	0.0357	0.0247	0.0315	0.1426	0.0638	-0.2488	-0.0249	0.0421	-0.0609	0.1966	0.0587	0.0336	0.3681	0.0822	-0.2891	-0.0443	-0.2375	0.5556	93.3027	46.4526	47.9513
6	0.2644	0.0139	0.0226	0.0905	-0.0279	0.1703	0.2075	0.1312	-0.3161	-0.0058	-0.0218	-0.027	0.2008	0.0454	0.1245	0.1798	0.0055	-0.0698	0.1684	-0.0854	0.164	83.2332	60.8528	44.1138
7	0.1029	0.0309	0.0396	0.0545	0.0179	0.0466	-0.052	0.0422	0.0888	-0.0022	-0.0185	0.0549	-0.0343	-0.1147	0.0372	0.239	-0.0474	-0.0886	0.2655	-0.0527	0.2657	63.4854	64.4683	50.2383
8	0.264	0.0045	0.0703	0.1395	0.1547	0.1837	0.0799	0.0056	0.1012	0.0365	-0.0341	-0.0328	0.0724	-0.0608	0.0047	0.1509	-0.0109	0.0384	0.1382	0.0329	0.1359	96.3218	86.3077	66.3302
9	0.1363	0.021	0.039	0.1156	0.0026	0.1893	0.0923	-0.0709	-0.0254	0.0992	-0.0599	0.0016	0.1393	-0.0345	0.0059	0.1556	-0.0343	-0.0162	0.1234	0.0057	0.0837	95.4893	73.2969	70.2913
10	0.0652	-0.0671	0.0355	0.2884	0.095	0.225	0.1182	0.004	0.2267	0.0606	-0.022	-0.194	0.0017	0.0137	0.064	0.0869	-0.0155	0.0289	0.0983	0.049	0.2	109.1756	86.1962	64.4791
11	0.031	0.0061	0.038	0.0093	-0.0068	0.0577	0.1085	0.0791	0.0962	-0.0829	-0.0437	-0.0718	-0.1202	-0.0201	-0.0011	0.2373	0.0307	0.1317	0.2809	0.1793	0.2996	109.6251	96.7187	43.3721
12	0.0601	0.0193	-0.0473	0.0068	-0.0229	0.0742	0.1156	0.1092	0.1208	-0.0755	-0.0169	-0.104	-0.0776	-0.0088	0.0381	0.0813	-0.007	0.2799	0.2783	0.2793	0.067	111.6104	89.682	40.5404
13	0.0632	0.0575	-0.0011	0.0825	-0.0374	0.1457	0.1315	0.2032	0.0415	-0.1123	-0.0607	-0.1105	-0.0083	0.0788	0.0283	0.1341	0.0356	0.0553	0.2234	0.0257	0.1371	109.3517	77.803	44.2798
14	0.2978	-0.1764	-0.0627	0.2373	0.0025	0.2164	0.0555	0.1348	0.123	-0.0756	-0.0443	-0.1123	-0.0529	0.1085	-0.0055	0.0894	0.0058	-0.0009	0.129	0.0055	0.1182	110.1998	77.1151	58.6889
15	0.0076	0.009	0.0163	0.0253	0.023	0.1021	0.0387	-0.0199	0.1281	0.0447	0.0247	-0.123	-0.0118	0.1473	-0.0373	0.1128	-0.0284	0.0071	0.1616	-0.0149	0.2548	111.1815	91.467	66.0072
16	0.1566	0.023	0.1174	0.1378	0.0366	0.2258	0.0368	-0.0665	0.018	0.1	-0.0058	-0.0827	-0.0296	0.0633	-0.0084	0.1657	-0.0187	-0.0434	0.194	-0.0253	0.1474	102.3062	85.7865	79.0364

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:51)	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 52:98)	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 99:130)	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 131:182)	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 183:237)	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 238:332)	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 333:363)	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 2:29)	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 30:98)	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 99:156)	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 157:182)	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 183:211)	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 212:259)	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 260:314)	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 315:346)	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 347:365)	B

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