PDB-3opf: Crystal structure of TTHA0988 in space group P212121

ID or keywords:

Entry

Database: PDB / ID: 3opf

Title

Crystal structure of TTHA0988 in space group P212121

Components

Putative uncharacterized protein TTHA0988

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / KipI / KipA / cyclophilin / allophanate hydrolase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses

Function / homology

Function and homology information

KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Cyclophilin-like / Cyclophilin ...
Similarity search - Domain/homology

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.95 Å

Authors

Jacques, D.A. / Kuramitsu, S. / Yokoyama, S. / Trewhella, J. / Guss, J.M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: The structure of TTHA0988 from Thermus thermophilus, a KipI-KipA homologue incorrectly annotated as an allophanate hydrolase
Authors: Jacques, D.A. / Langley, D.B. / Kuramitsu, S. / Yokoyama, S. / Trewhella, J. / Guss, J.M.

History

Deposition	Sep 1, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 2, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3opf.cif.gz	572.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3opf.ent.gz	472.6 KB	Display	PDB format
PDBx/mmJSON format	3opf.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/op/3opf ftp://data.pdbj.org/pub/pdb/validation_reports/op/3opf	HTTPS FTP

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Related structure data

Related structure data	3oepC 3oreSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ez4-1 5cku-d 2fy2-d 3cch-1 5t6y-d 4l3c-12 6co6-d 6coj-d 4l29-13 6jj4-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: ttk003001624.1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Putative uncharacterized protein TTHA0988

B: Putative uncharacterized protein TTHA0988

C: Putative uncharacterized protein TTHA0988

hetero molecules

160 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein TTHA0988

hetero molecules

defined by author&software
53.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative uncharacterized protein TTHA0988

hetero molecules

defined by author&software
53.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Putative uncharacterized protein TTHA0988

hetero molecules

defined by author&software
53.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.505, 132.107, 177.833
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative uncharacterized protein TTHA0988 Mass: 53157.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0988 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q5SJM0
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1159 / 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: 2.74 Å³/Da / Density % sol: 55.17 % / Mosaicity: 0.185 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.17M ammonium sulfate, 0.085M sodium cacodylate, 25.5% PEG 8000, 15% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL44B2 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2004

Radiation

Monochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. all: 111600 / Num. obs: 111600 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / B_iso Wilson estimate: 26.7 Å² / R_merge(I) obs: 0.131 / Χ²: 1.028 / Net I/σ(I): 11.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.95-1.98	4.2	0.606	2.3	3250	1.094	51.6
1.98-2.02	4.3	0.54	2.6	3584	1.082	56.6
2.02-2.06	4.3	0.492	2.9	4016	1.09	63.8
2.06-2.1	4.3	0.443	3.2	4708	1.081	74.4
2.1-2.15	4.4	0.412	3.5	5559	1.067	87.8
2.15-2.2	4.4	0.367	3.8	5519	1.032	86.9
2.2-2.25	4.4	0.346	4.1	5529	1.085	87.5
2.25-2.31	4.3	0.317	4.4	5589	1.075	88
2.31-2.38	4.3	0.294	4.6	5633	1.08	88.8
2.38-2.46	4.2	0.268	4.8	5718	1.066	90.2
2.46-2.54	4.2	0.244	5	5878	1.045	92.2
2.54-2.65	4.2	0.224	5.1	6016	1.008	94.5
2.65-2.77	4.2	0.196	5.7	6147	1.008	96.4
2.77-2.91	4.3	0.179	6.2	6239	0.951	98
2.91-3.1	4.5	0.161	7.6	6282	1.05	98.1
3.1-3.33	4.7	0.146	8.5	6332	1.001	98.8
3.33-3.67	4.9	0.129	9.6	6354	0.986	98.6
3.67-4.2	5	0.113	10.8	6361	0.99	98.3
4.2-5.29	5	0.099	12	6431	0.948	98.2
5.29-50	4.8	0.07	15.9	6455	0.977	94.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 51.14 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.31 Å	33.05 Å
Translation	2.31 Å	33.05 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.1.4	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
ADSC	Quantum	data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ORE

3ore

Resolution: 1.95→33.05 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.937 / WR_factor R_free: 0.2333 / WR_factor R_work: 0.1972 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8511 / SU B: 8.034 / SU ML: 0.104 / SU R Cruickshank DPI: 0.1914 / SU R_free: 0.1657 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2333	5548	5 %	RANDOM
R_work	0.1972	-	-	-
all	0.199	110890	-	-
obs	0.199	110890	86.57 %	-

Solvent computation

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

Displacement parameters

B_iso max: 71.03 Å² / B_iso mean: 38.991 Å² / B_iso min: 12.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.71 Å²	0 Å²	0 Å²
2-	-	-4.02 Å²	0 Å²
3-	-	-	3.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→33.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11026	0	39	1159	12224

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	11404
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8186
X-RAY DIFFRACTION	r_angle_refined_deg	1.107	2.027	15581
X-RAY DIFFRACTION	r_angle_other_deg	0.785	3	19785
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.504	5	1472
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.508	21.002	439
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.364	15	1644
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.797	15	133
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1689
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.022	12802
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2367
X-RAY DIFFRACTION	r_mcbond_it	1.161	2	7361
X-RAY DIFFRACTION	r_mcbond_other	0.336	2	2940
X-RAY DIFFRACTION	r_mcangle_it	1.859	3	11758
X-RAY DIFFRACTION	r_scbond_it	2.731	4	4043
X-RAY DIFFRACTION	r_scangle_it	4.186	6	3820

LS refinement shell

Resolution: 1.951→2.002 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	240	-
R_work	0.257	4500	-
all	-	4740	-
obs	-	-	50.62 %

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	2.0566	0.4876	-0.4231	3.796	0.6136	2.8235	-0.0363	-0.2324	-0.2457	0.4625	0.0422	-0.413	0.4642	0.3627	-0.006	0.22	0.1073	-0.0759	0.2262	0.0338	0.0827	41.283	16.657	18.9627
2	0.574	0.1871	-0.3366	1.7286	0.4657	1.5229	-0.0546	-0.0395	0.004	-0.0585	0.0924	-0.0785	-0.0235	0.1076	-0.0379	0.0215	-0.0202	0.0012	0.12	-0.0216	0.028	36.9053	37.9213	2.6181
3	0.685	0.2065	0.0688	1.4628	0.394	0.4904	-0.1233	0.0345	-0.1017	-0.0722	0.0708	0.0215	0.0144	0.0097	0.0525	0.071	-0.0063	0.0419	0.113	0.0037	0.0328	20.6742	3.0692	-2.3983
4	1.7038	0.9976	-0.3536	1.762	0.0454	1.0833	0.0467	-0.1552	0.0677	0.2881	-0.0621	0.1084	-0.0446	0.0424	0.0154	0.1493	0.0511	0.0242	0.1511	0.005	0.008	17.8351	18.9447	19.5243
5	2.4303	-0.3881	0.3316	3.1327	-0.1102	2.6575	0.0546	0.3183	0.0391	-0.4277	0.0663	-0.2117	0.0168	0.2361	-0.1209	0.1743	0.0155	0.017	0.1989	-0.0453	0.029	63.6453	-3.8655	44.9309
6	0.8464	0.2137	-0.1805	1.3606	-0.2503	0.7099	0.0224	-0.0212	-0.0149	0.0354	0.0158	0.0462	-0.0068	0.0494	-0.0382	0.0752	0.0006	-0.0132	0.1495	-0.0204	0.009	59.4342	-2.1373	71.8253
7	0.8745	-0.4846	0.7168	1.8311	-0.2698	1.6939	-0.055	-0.0119	0.0756	-0.0507	0.0185	0.0606	-0.2395	-0.1953	0.0365	0.1191	0.0274	-0.0182	0.1487	0.0105	0.0173	43.4464	21.7826	46.2676
8	1.8067	-0.1718	0.9198	2.257	-0.1747	1.3508	0.0459	0.0484	-0.1563	-0.2035	0.1232	0.3543	0.1559	-0.1229	-0.1691	0.1173	-0.056	-0.0513	0.1607	0.0142	0.074	39.8289	-5.3009	46.8293
9	1.7559	-0.5328	-0.5017	3.4772	0.7823	3.8396	0.0025	-0.148	0.0002	0.1366	0.0313	-0.3948	-0.2761	0.2068	-0.0339	0.1342	-0.0357	0.0293	0.0955	0.0151	0.0878	90.5357	-18.0111	16.2515
10	1.5587	0.6311	-0.3656	1.7729	0.282	1.2577	-0.0407	0.1384	0.1341	-0.1855	0.0843	0.2683	-0.195	-0.0454	-0.0437	0.1206	0.0264	-0.0154	0.0991	0.0439	0.0583	82.0722	-40.5488	2.0033
11	0.9763	-0.9151	-0.7143	2.0077	0.61	2.3385	-0.168	-0.0997	-0.2143	0.1276	-0.1054	0.2549	0.0207	-0.0794	0.2734	0.0958	0.0143	0.0407	0.1312	-0.0232	0.0668	65.4172	-29.0906	34.5691
12	2.2069	-0.6077	-0.4348	1.4463	-0.4289	1.2491	-0.1985	0.0465	0.328	-0.0846	0.0752	-0.1889	-0.2624	-0.1079	0.1232	0.2721	0.0594	-0.064	0.1268	-0.0171	0.0823	67.0698	-14.6802	11.4402

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 70
2	X-RAY DIFFRACTION	2	A	71 - 210
3	X-RAY DIFFRACTION	3	A	211 - 386
4	X-RAY DIFFRACTION	4	A	387 - 493
5	X-RAY DIFFRACTION	5	B	1 - 70
6	X-RAY DIFFRACTION	6	B	71 - 210
7	X-RAY DIFFRACTION	7	B	211 - 386
8	X-RAY DIFFRACTION	8	B	387 - 493
9	X-RAY DIFFRACTION	9	C	1 - 70
10	X-RAY DIFFRACTION	10	C	76 - 210
11	X-RAY DIFFRACTION	11	C	211 - 386
12	X-RAY DIFFRACTION	12	C	387 - 493

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