PDB-4fbd: 2.35 Angstrom Crystal Structure of Conserved Hypothetical Protein...

ID or keywords:

Entry

Database: PDB / ID: 4fbd

Title

2.35 Angstrom Crystal Structure of Conserved Hypothetical Protein from Toxoplasma gondii ME49.

Components

Putative uncharacterized protein

Keywords

UNKNOWN FUNCTION / Conserved Hypothetical /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Protein of unknown function (DUF3228), domain 1 / YaeB-like fold / 2-Layer Sandwich / Alpha Beta / :

Function and homology information

Biological species

Toxoplasma gondii (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Minasov, G. / Ruan, J. / Wawrzak, Z. / Shuvalova, L. / Ngo, H. / Knoll, L. / Milligan-Myhre, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: 2.35 Angstrom Crystal Structure of Conserved Hypothetical Protein from Toxoplasma gondii ME49.
Authors: Minasov, G. / Ruan, J. / Wawrzak, Z. / Shuvalova, L. / Ngo, H. / Knoll, L. / Milligan-Myhre, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	May 22, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fbd.cif.gz	180.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4fbd.ent.gz	145.3 KB	Display	PDB format
PDBx/mmJSON format	4fbd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fb/4fbd ftp://data.pdbj.org/pub/pdb/validation_reports/fb/4fbd	HTTPS FTP

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Related structure data

Related structure data	2pd0S S: Starting model for refinement
Similar structure data	5vjq-1 6p4b-2 1xgt-d 1xgu-d 5vjq-2 6cbv-d 5vjo-1 5eii-1 5x8l-2 3jtj-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP90278

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative uncharacterized protein

B: Putative uncharacterized protein

54.2 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)	47.599, 87.216, 112.122
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative uncharacterized protein Mass: 27108.758 Da / Num. of mol.: 2 Fragment: Conserved Hypothetical Protein from Toxoplasma gondii ME49 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGME49_003450, TGVEG_045980 / Plasmid: pCCK-N'-6XHisTag-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Magic / References: UniProt: B6KHY2
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative uncharacterized protein

Mass: 27108.758 Da / Num. of mol.: 2
Fragment: Conserved Hypothetical Protein from Toxoplasma gondii ME49
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGME49_003450, TGVEG_045980 / Plasmid: pCCK-N'-6XHisTag-TEV / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21DE3 Magic / References: UniProt: B6KHY2

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.15 Å³/Da / Density % sol: 42.69 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 7.0mg/mL, 0.5M Sodium cloride, Tris-HCl pH 8.3; Screen: JCSG+ (F11), 1M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1.0% (w/v) PEG MME 2000; Cryo: Screen solution : 50% Sucrose, 1:1 ...Details: Protein: 7.0mg/mL, 0.5M Sodium cloride, Tris-HCl pH 8.3; Screen: JCSG+ (F11), 1M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1.0% (w/v) PEG MME 2000; Cryo: Screen solution : 50% Sucrose, 1:1 (v/v), VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 42.69 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 7.0mg/mL, 0.5M Sodium cloride, Tris-HCl pH 8.3; Screen: JCSG+ (F11), 1M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1.0% (w/v) PEG MME 2000; Cryo: Screen solution : 50% Sucrose, 1:1 ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2011 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.35→30 Å / Num. all: 20165 / Num. obs: 20165 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / B_iso Wilson estimate: 58.5 Å² / R_merge(I) obs: 0.066 / Net I/σ(I): 27.6
Reflection shell	Resolution: 2.35→2.39 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.557 / Mean I/σ(I) obs: 3.9 / Num. unique all: 983 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHENIX		model building
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2PD0

2pd0

Resolution: 2.35→29.4 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.926 / SU B: 15.767 / SU ML: 0.171
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25826	1026	5.1 %	RANDOM
R_work	0.20232	-	-	-
all	0.20509	19076	-	-
obs	0.20509	19076	99.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 53.823 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.51 Å²	0 Å²	-0 Å²
2-	-	1.53 Å²	0 Å²
3-	-	-	-1.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→29.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3172	0	0	98	3270

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	3294
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2252
X-RAY DIFFRACTION	r_angle_refined_deg	1.471	1.977	4489
X-RAY DIFFRACTION	r_angle_other_deg	0.851	3	5489
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.609	5	406
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	22.658	23.724	145
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.99	15	536
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.074	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	497
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3654
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	662
X-RAY DIFFRACTION	r_mcbond_it	1.235	1.5	2051
X-RAY DIFFRACTION	r_mcbond_other	0.289	1.5	800
X-RAY DIFFRACTION	r_mcangle_it	2.223	2	3316
X-RAY DIFFRACTION	r_scbond_it	3.053	3	1243
X-RAY DIFFRACTION	r_scangle_it	4.433	4.5	1173

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	72	-
R_work	0.273	1382	-
obs	-	1382	99.86 %

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	2.6622	-0.3175	0.22	4.6581	2.8712	6.9739	-0.0408	-0.3317	0.5125	-0.0565	-0.0777	0.0428	-0.4628	-0.0704	0.1185	0.1966	0.0272	0.0404	0.1315	-0.0613	0.1783	15.8203	-6.5381	17.3904
2	4.0044	1.1729	-2.1083	1.4411	-0.4341	4.1069	0.0836	0.0334	0.4134	0.0124	0.0597	0.1728	-0.4079	0.0498	-0.1432	0.0629	-0.0061	-0.017	0.0147	0.01	0.0652	7.8287	-13.794	-8.7768
3	3.5274	0.4597	1.7938	3.4617	4.3519	5.9404	-0.0358	0.0102	0.2829	-0.6357	0.066	-0.1632	-0.8181	-0.0529	-0.0302	0.2408	0.0346	-0.0304	0.2643	-0.0824	0.136	14.7268	-10.0938	11.7619
4	6.1674	0.8659	-1.814	11.7822	-1.9438	3.8228	-0.3185	0.4774	0.3905	-2.5031	-0.0434	-0.0066	0.223	0.17	0.3619	1.0067	-0.1066	-0.0172	0.5115	-0.081	0.4768	21.5977	11.8281	13.4232
5	7.1964	8.9564	6.243	18.9358	16.3307	15.3463	-0.2684	0.0938	0.1741	-1.6547	0.1204	-0.0369	-1.6534	-0.0663	0.1481	0.3034	0.0497	0.0448	0.1124	-0.0661	0.1624	17.0124	-4.3546	13.4544
6	4.5409	-2.6501	3.3872	4.4024	2.6425	10.0724	-0.3834	-0.0613	0.2134	0.2667	0.1221	-0.142	-0.254	0.0798	0.2613	0.0687	-0.0262	-0.0414	0.1417	-0.0535	0.2301	20.2814	-15.3173	4.1486
7	6.0118	0.25	-0.8008	6.2628	-1.3567	5.4714	-0.1224	0.1604	1.0052	-0.1902	0.1722	-0.4193	-0.6645	0.6541	-0.0498	0.1187	-0.1043	-0.0094	0.2055	-0.0077	0.2548	25.4414	-9.9469	-8.4542
8	10.5692	-1.2115	1.7252	0.9909	1.9843	5.9406	0.0694	0.4561	0.9029	-0.3591	-0.1062	-0.1094	-0.844	-0.1248	0.0368	0.2246	-0.0043	0.0161	0.138	0.1125	0.2962	4.9473	-12.1709	-10.1253
9	10.3471	-0.6542	-1.4193	3.7623	2.2936	4.4235	-0.1617	1.0047	-0.1899	-0.4034	0.0338	-0.2067	-0.1707	0.1041	0.1279	0.4611	0.0049	-0.0515	0.4627	0.0404	0.2338	24.6942	-20.2531	-44.0085
10	4.2291	0.1478	0.9785	1.4843	0.371	4.0492	0.0201	0.4899	-0.1349	-0.1918	0.0869	-0.0548	0.144	0.2459	-0.107	0.0972	-0.0202	0.0141	0.1314	0.0305	0.0561	12.8025	-21.2338	-21.845
11	29.8779	0.6321	-5.9293	0.1032	-0.7385	5.507	-0.3162	0.1861	0.6475	-0.0057	0.0277	-0.0384	-0.1288	-0.3528	0.2885	0.3381	0.0464	-0.0657	0.3938	0.0376	0.1547	18.8436	-18.8806	-40.2573
12	12.7278	-0.5395	4.8163	5.2742	-0.8857	9.6903	-0.1884	0.792	0.1539	-0.3546	-0.0477	-0.0409	0.181	-0.1296	0.2361	0.2148	-0.0306	0.0201	0.3569	0.057	0.1292	41.5535	-18.5952	-37.2223
13	19.2806	1.3761	-1.8009	2.6654	0.1733	1.3383	0.1415	0.5666	0.1258	0.1019	-0.0767	-0.1497	-0.2673	-0.1944	-0.0648	0.2556	0.0149	-0.002	0.2859	0.0365	0.0469	25.4787	-18.7195	-40.6761
14	0.2019	-1.2783	0.3817	9.8165	-2.9017	29.5316	0.294	0.1156	0.0133	-1.1926	-0.0356	0.0218	-1.4839	0.5335	-0.2584	0.5284	0.0913	0.1024	0.5116	0.0379	0.5393	15.8924	-10.9845	-35.1489
15	12.8167	5.7081	4.8001	3.1766	3.6792	11.2013	0.0243	0.5622	0.0269	-0.2698	0.278	-0.479	-0.6966	1.1404	-0.3022	0.423	-0.1494	0.0656	0.3313	0.1546	0.5961	21.7636	-5.8098	-22.2622
16	2.1317	1.4922	-0.0854	5.7934	-2.2426	7.5652	0.0225	0.007	-0.3088	0.1826	-0.1399	-0.2276	0.4216	0.4308	0.1174	0.2728	-0.0285	0.0306	0.2771	0.023	0.2209	13.1473	-24.1136	-20.1851

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 87
2	X-RAY DIFFRACTION	2	A	88 - 128
3	X-RAY DIFFRACTION	3	A	129 - 140
4	X-RAY DIFFRACTION	4	A	141 - 161
5	X-RAY DIFFRACTION	5	A	162 - 174
6	X-RAY DIFFRACTION	6	A	175 - 182
7	X-RAY DIFFRACTION	7	A	183 - 214
8	X-RAY DIFFRACTION	8	A	215 - 227
9	X-RAY DIFFRACTION	9	B	15 - 87
10	X-RAY DIFFRACTION	10	B	88 - 128
11	X-RAY DIFFRACTION	11	B	129 - 140
12	X-RAY DIFFRACTION	12	B	141 - 161
13	X-RAY DIFFRACTION	13	B	162 - 174
14	X-RAY DIFFRACTION	14	B	175 - 182
15	X-RAY DIFFRACTION	15	B	183 - 214
16	X-RAY DIFFRACTION	16	B	215 - 227

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