PDB-4ml9: Crystal Structure of Uncharacterized TIM Barrel Protein with the ...

ID or keywords:

Entry

Database: PDB / ID: 4ml9

Title

Crystal Structure of Uncharacterized TIM Barrel Protein with the Conserved Phosphate Binding Site fromSebaldella termitidis

Components

Uncharacterized protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / TIM barrel / PSI-Biology

Function / homology

Function and homology information

L-histidine biosynthetic process / metal ion binding
Similarity search - Function

Biological species

Sebaldella termitidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.841 Å

Authors

Kim, Y. / Holowicki, J. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal Structure of Uncharacterized TIM Barrel Protein with the Conserved Phosphate Binding Site fromSebaldella termitidis
Authors: Kim, Y. / Holowicki, J. / Endres, M. / Joachimiak, A.

History

Deposition	Sep 6, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 18, 2013	Provider: repository / Type: Initial release
Revision 1.1	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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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	4ml9.cif.gz	243.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ml9.ent.gz	199.9 KB	Display	PDB format
PDBx/mmJSON format	4ml9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ml9_validation.pdf.gz	465.7 KB	Display	wwPDB validaton report
Full document	4ml9_full_validation.pdf.gz	470 KB	Display
Data in XML	4ml9_validation.xml.gz	31.9 KB	Display
Data in CIF	4ml9_validation.cif.gz	44.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ml/4ml9 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/4ml9	HTTPS FTP

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Related structure data

Similar structure data	3h2c-2 4cxx-d 5j6d-d 3tyd-2 4d9p-2 3hwp-d 3k5w-d 5u14-d 6q62-1 2bnf-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-APC103744

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

63.3 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)	127.475, 127.475, 91.013
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-523- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Uncharacterized protein Mass: 30983.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sebaldella termitidis (bacteria) / Strain: ATCC 33386 / Gene: Sterm_2790 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D1AMR0

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Non-polymers , 5 types, 539 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#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.: 518 / 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: 2.98 Å³/Da / Density % sol: 58.77 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M magnesium chloride, 0.1 M MES pH 6.5, 30 %(w/v) PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012 / Details: mirrors
Radiation	Monochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97895 Å / Relative weight: 1
Reflection	Resolution: 1.84→50 Å / Num. all: 64381 / Num. obs: 64381 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / B_iso Wilson estimate: 21.5 Å² / R_sym value: 0.066 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.84→1.87 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 3161 / R_sym value: 0.773 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELXS		phasing
MLPHARE		phasing
DM		model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.841→31.869 Å / SU ML: 0.14 / Isotropic thermal model: mmixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.55 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.176	3217	5.06 %	rando
R_work	0.151	-	-	-
all	0.152	63528	-	-
obs	0.152	63528	97.37 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 25.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.841→31.869 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4138	0	87	518	4743

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4558
X-RAY DIFFRACTION	f_angle_d	1.183	6163
X-RAY DIFFRACTION	f_dihedral_angle_d	13.994	1714
X-RAY DIFFRACTION	f_chiral_restr	0.082	710
X-RAY DIFFRACTION	f_plane_restr	0.005	810

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
1.8411-1.8686	0.2133	123	0.1978	2143	2266	81
1.8686-1.8978	0.2116	141	0.1777	2470	2611	93
1.8978-1.9289	0.2014	142	0.1754	2519	2661	96
1.9289-1.9622	0.2375	135	0.1698	2556	2691	96
1.9622-1.9978	0.2258	125	0.1645	2563	2688	97
1.9978-2.0363	0.1992	135	0.1612	2654	2789	99
2.0363-2.0778	0.2048	157	0.1568	2601	2758	99
2.0778-2.123	0.1909	136	0.1509	2657	2793	99
2.123-2.1724	0.1716	120	0.1535	2664	2784	99
2.1724-2.2267	0.1573	116	0.1462	2680	2796	100
2.2267-2.2869	0.1692	141	0.1433	2658	2799	100
2.2869-2.3541	0.1733	138	0.1461	2661	2799	100
2.3541-2.4301	0.1896	150	0.1424	2643	2793	99
2.4301-2.5169	0.163	143	0.1425	2648	2791	99
2.5169-2.6176	0.1662	128	0.1422	2676	2814	99
2.6176-2.7367	0.182	158	0.1553	2647	2815	99
2.7367-2.8809	0.1985	153	0.1548	2656	2809	99
2.8809-3.0613	0.19	148	0.1601	2660	2808	99
3.0613-3.2974	0.1617	139	0.1581	2668	2817	99
3.2974-3.6288	0.1604	154	0.1407	2676	2830	98
3.6288-4.1529	0.1504	137	0.1342	2691	2828	98
4.1529-5.2285	0.1496	144	0.1359	2715	2859	98
5.2285-31.8735	0.1844	154	0.165	2805	2959	96

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	4.0043	3.924	-3.6802	6.1101	-5.0014	4.2767	0.0211	0.217	0.0922	-0.0002	0.2372	0.3743	-0.1809	-0.4924	-0.2844	0.1501	0.0588	-0.0513	0.2334	-0.0376	0.1685	14.4754	48.382	5.9144
2	4.1307	0.1819	0.4081	2.1386	-0.6495	2.0916	-0.0867	-0.1328	-0.1071	0.0507	0.1197	0.1463	0.0391	-0.1771	-0.0296	0.1058	0.0334	-0.0138	0.1306	-0.0193	0.1244	22.4767	35.3488	19.1317
3	3.6146	0.0266	2.5353	3.0236	-0.0916	2.7775	-0.0988	-0.1517	0.285	0.3265	-0.0757	-0.0953	-0.2082	-0.0514	0.1642	0.1372	0.041	-0.0105	0.1346	-0.0454	0.1702	35.7559	43.5527	21.5612
4	4.7568	1.2252	1.7851	4.9006	2.0832	6.2146	-0.2712	-0.1893	0.7594	-0.0139	-0.0723	0.0112	-0.6966	0.2165	0.2786	0.1982	0.0693	-0.0695	0.1491	-0.0196	0.2792	28.7884	49.9186	16.7345
5	3.9763	-0.5327	-1.5986	3.4161	1.2872	4.9854	-0.0404	0.1258	0.4008	-0.0137	-0.1156	-0.2185	-0.3892	0.323	0.117	0.1563	0.0216	-0.0708	0.1516	0.0298	0.1945	28.4417	52.8258	12.2638
6	2.0258	0.0036	-1.7712	1.5504	2.1393	6.0206	0.0054	-0.3702	0.3971	0.1951	0.027	-0.1022	-0.5458	0.4214	-0.0476	0.3004	0.0603	-0.0673	0.2175	-0.073	0.263	22.2375	57.944	22.2747
7	3.6935	-0.122	-0.3367	3.1889	0.8927	3.5347	-0.0167	-0.3848	0.119	0.2895	-0.0998	0.3599	-0.2196	-0.3425	0.0533	0.2757	0.1233	0.0035	0.3184	-0.1053	0.2464	12.1025	53.5598	28.0012
8	8.4719	0.7103	-1.3849	4.7122	-0.302	6.0605	-0.0142	-0.5331	-0.6118	0.4803	-0.0601	0.3907	0.1421	-0.3723	0.0786	0.1869	0.0598	0.0454	0.2599	0.0093	0.2344	13.3866	40.2564	30.589
9	7.5661	-6.8473	2.0726	7.4699	-2.0693	3.59	-0.6568	-0.528	-0.4227	0.8795	0.7364	0.3992	0.0924	-0.3116	-0.0953	0.2165	-0.001	0.0413	0.2323	0.0315	0.17	31.1194	22.4912	32.3767
10	6.2209	4.435	-2.3287	3.3028	-1.585	6.5424	0.012	-0.0812	0.1602	0.0752	-0.0182	-0.1021	-0.3726	0.1686	0.0193	0.12	0.0274	-0.0306	0.122	0.0024	0.1414	58.0258	21.286	31.5716
11	1.7961	-1.0153	0.765	2.0157	-1.0502	2.2332	0.0228	-0.0337	0.0366	-0.0179	-0.0557	0.087	-0.0869	-0.1327	0.027	0.0871	0.0205	0.0023	0.0878	-0.0163	0.109	39.8298	25.6362	22.0395
12	2.558	-0.9619	1.2245	1.0672	0.3076	5.643	0.0875	0.1433	0.0093	-0.1934	-0.1309	-0.0541	-0.2478	-0.0932	0.049	0.1456	0.0482	-0.0066	0.0868	0.0158	0.1633	43.7339	29.8875	14.2508
13	2.2608	-0.3774	0.0606	2.5002	1.1834	3.668	0.0027	0.2968	0.1301	-0.1732	0.0417	-0.1822	-0.4607	0.5552	-0.0574	0.1128	-0.0095	-0.0015	0.1189	0.0301	0.1385	51.1258	25.9804	14.1586
14	1.2805	0.8127	0.3368	4.4643	1.2204	2.3409	0.001	0.1301	0.1169	-0.1975	-0.0513	-0.1311	-0.1635	0.1999	0.0479	0.0696	0.0179	0.0058	0.1144	0.038	0.1015	55.4124	20.0202	12.8074
15	4.8095	3.8643	1.419	7.6199	2.2448	2.9044	0.0553	0.2469	-0.4541	-0.0635	0.1503	-0.8518	0.2417	0.4289	-0.1783	0.1095	0.0467	0.0186	0.1601	-0.0056	0.1645	59.0639	5.509	14.5291
16	3.2083	0.7503	-0.2606	3.4956	0.2078	2.6338	-0.0098	0.0278	-0.1095	0.009	-0.0378	0.232	0.1808	-0.2472	0.0408	0.0915	0	0.0046	0.0849	0.0143	0.0909	44.0174	6.4769	21.0376
17	7.1698	-6.0599	-0.9379	7.0993	0.867	3.4959	0.1162	0.1789	-0.8656	-0.0048	-0.1585	0.7712	0.0742	-0.4454	0.0532	0.1152	-0.0327	-0.017	0.1711	-0.0116	0.2077	23.5632	24.8848	23.8009

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 56 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 98 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 99 through 121 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 122 through 142 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 143 through 179 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 180 through 236 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 237 through 258 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 259 through 281 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 4 through 23 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 24 through 71 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 72 through 98 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 99 through 121 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 122 through 179 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 180 through 193 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 194 through 258 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 259 through 278 )

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