PDB-3ore: Crystal structure of TTHA0988 in space group P6522

ID or keywords:

Entry

Database: PDB / ID: 3ore

Title

Crystal structure of TTHA0988 in space group P6522

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

hydrolase activity / ATP binding
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

MIRAS / Resolution: 2.9 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 7, 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	Mar 20, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ore.cif.gz	287.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3ore.ent.gz	233.3 KB	Display	PDB format
PDBx/mmJSON format	3ore.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ore_validation.pdf.gz	437.1 KB	Display	wwPDB validaton report
Full document	3ore_full_validation.pdf.gz	443.2 KB	Display
Data in XML	3ore_validation.xml.gz	25.3 KB	Display
Data in CIF	3ore_validation.cif.gz	34.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/or/3ore ftp://data.pdbj.org/pub/pdb/validation_reports/or/3ore	HTTPS FTP

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Related structure data

Related structure data	3oepC 3opfC C: citing same article (ref.)
Similar structure data	3opf-2 4l3c-1 4l29-11 4prb-d 1dfc-2 3tby-1 2xja-3 3tzy-1 1ulz-d 3sut-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&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

106 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein TTHA0988

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

2

B: Putative uncharacterized protein TTHA0988

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

Unit cell

Length a, b, c (Å)	142.071, 142.071, 259.133
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Putative uncharacterized protein TTHA0988 Mass: 53157.391 Da / Num. of mol.: 2 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

#1: Protein

Putative uncharacterized protein TTHA0988

Mass: 53157.391 Da / Num. of mol.: 2
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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.55 Å³/Da / Density % sol: 65.36 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 3.3M NaCl, 0.04M HEPES, 4.6%(v/v) 1-propanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å

Detector

Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 26, 2009 / Details: OSMIC MIRRORS

Radiation

Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Redundancy: 6.7 % / Av σ(I) over netI: 21.07 / Number: 162025 / R_merge(I) obs: 0.126 / Χ²: 1.03 / D res high: 3.3 Å / D res low: 50 Å / Num. obs: 24022 / % possible obs: 99.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
8.94	50	97.9	1	0.094	1.064	6.4
7.1	8.94	99.5	1	0.098	1.045	7
6.21	7.1	99.6	1	0.108	1.008	7.1
5.64	6.21	99.6	1	0.114	1.033	7.1
5.24	5.64	99.8	1	0.118	0.965	7.2
4.93	5.24	99.9	1	0.116	0.952	7.2
4.68	4.93	100	1	0.119	1.01	7.2
4.48	4.68	100	1	0.126	0.987	7.2
4.31	4.48	100	1	0.13	1.021	7.2
4.16	4.31	100	1	0.138	1.033	7.2
4.03	4.16	100	1	0.147	1.051	7.3
3.91	4.03	100	1	0.163	1.078	7.2
3.81	3.91	100	1	0.17	1.048	7.2
3.72	3.81	99.9	1	0.18	1.038	7.1
3.63	3.72	99.9	1	0.191	1.044	6.9
3.55	3.63	100	1	0.203	1.087	6.6
3.48	3.55	99.8	1	0.217	1.067	6.2
3.42	3.48	98.8	1	0.23	1.089	5.6
3.36	3.42	96.2	1	0.231	1.063	5
3.3	3.36	90.2	1	0.241	1.07	4.5

Reflection

Resolution: 2.9→50 Å / Num. all: 32167 / Num. obs: 32167 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / B_iso Wilson estimate: 59.9 Å² / R_merge(I) obs: 0.078 / Χ²: 1.032 / Net I/σ(I): 15.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.9-2.95	3.3	0.296	2.8	702	1.077	41.4
2.95-3	3.9	0.29	3.2	896	1.108	51.8
3-3.06	4.5	0.25	3.9	1118	1.026	66.2
3.06-3.12	4.9	0.26	4.3	1407	1.057	81.6
3.12-3.19	5.4	0.236	5.4	1591	1.067	93.3
3.19-3.27	6.3	0.214	7.3	1694	1.076	98.8
3.27-3.35	7.2	0.199	9.6	1722	1.09	100
3.35-3.44	7.8	0.173	11.7	1748	1.064	100
3.44-3.54	7.9	0.157	13.3	1719	1.061	100
3.54-3.65	8	0.131	16.1	1734	1.061	100
3.65-3.78	7.9	0.11	18.5	1719	1.069	100
3.78-3.94	8	0.1	20.3	1737	1.072	100
3.94-4.11	7.9	0.087	22.1	1741	1.001	100
4.11-4.33	7.9	0.073	24.9	1749	1.007	100
4.33-4.6	7.9	0.064	27.4	1758	0.95	100
4.6-4.96	7.9	0.058	31.2	1766	1.03	100
4.96-5.46	7.8	0.059	31.1	1778	0.995	99.9
5.46-6.24	7.7	0.06	29.9	1799	1.015	100
6.24-7.86	7.7	0.051	33	1834	0.99	99.8
7.86-50	7.1	0.04	35.3	1955	0.969	98.7

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Phasing

Phasing

Method:

MIRAS

Phasing MIR der

ID	Der set-ID
1	1
2	1
3	1
4	1
5	1
6	1
7	1
8	1
9	1

Phasing MIR der site

ID	Der-ID	B_iso (Å)	Atom type symbol	Fract x	Fract y	Fract z	Occupancy
1	1	60	Pt	0.8611	0.1914	0.051	0.3072
1	2	55.41	Pt	0.4001	0.8045	0.0697	0.1971
1	3	60	Pt	0.7338	0.5496	0.0032	0.2634
1	4	60	Pt	0.5025	0.4384	0.0561	0.2684
1	5	60	Pt	0.4912	0.4398	0.0421	0.2494
1	6	60	Pt	0.748	0.2349	0.0829	0.2174
1	7	60	Pt	0.6132	0.0768	0.008	0.225
1	8	60	Pt	0.8422	0.1966	0.0145	0.1858
1	9	60	Pt	0.5691	0.2037	0.0552	0.2158
2	1	60	U	0.05	0.3854	0.0217	0.1337
2	2	60	U	0.9617	0.4139	0.0134	0.1401
2	3	33.5141	U	0.8488	0.1882	0.0592	0.0347
2	4	42.5923	U	0.0532	0.3991	0.0048	0.0431
2	5	60	U	0.3965	0.2297	0.0193	0.0568
3	1	59.2724	Pb	0.535	0.2449	0.013	0.186
3	2	60	Pb	0.9528	0.4262	0.0384	0.2173
3	3	60	Pb	0.8365	0.4021	0.0047	0.1683
3	4	60	Pb	0.6565	0.0506	0.0225	0.1372
3	5	60	Pb	0.6994	0.5977	0.0481	0.1613
3	6	60	Pb	0.703	0.5802	0.0177	0.1369
3	7	54.5601	Pb	0.6554	0.0343	0.0524	0.1097
3	8	60	Pb	0.8735	0.2797	0.0126	0.1472
3	9	56.9784	Pb	0.0392	0.4913	0.006	0.085
4	1	46.4305	Hg	0.5054	0.452	0.0567	0.1346
5	1	60	U	0.0462	0.3831	0.021	0.1134
5	2	60	U	0.9621	0.4114	0.0134	0.0558
5	3	60	U	0.8535	0.1851	0.0567	0.1101
5	4	60	U	0.5216	0.456	0.0597	0.0713
5	5	10.5864	U	0.5452	0.4667	0.06	0.0255
6	1	60	I	0.8544	0.2761	0.0103	0.5277
6	2	60	I	0.6943	0.3296	0.03	0.3744
6	3	60	I	0.4862	0.3358	0.0155	0.3096
6	4	16.119	I	0.5643	0.2151	0.0477	0.093

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.1	phasing
RESOLVE		phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
MAR345dtb		data collection

Refinement

Method to determine structure:

MIRAS / Resolution: 2.9→47.87 Å / Cor.coef. F_o:F_c: 0.872 / Cor.coef. F_o:F_c free: 0.847 / WR_factor R_free: 0.3034 / WR_factor R_work: 0.2757 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8141 / SU B: 39.881 / SU ML: 0.337 / SU R Cruickshank DPI: 0.6868 / SU R_free: 0.4063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.406
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3162	1625	5.1 %	RANDOM
R_work	0.2847	-	-	-
all	0.2863	30462	-	-
obs	0.2863	30462	91.74 %	-

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 max: 68.45 Å² / B_iso mean: 70.794 Å² / B_iso min: 10.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.8 Å²	0.9 Å²	0 Å²
2-	-	1.8 Å²	0 Å²
3-	-	-	-2.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→47.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5454	0	0	0	5454

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	5608
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3971
X-RAY DIFFRACTION	r_angle_refined_deg	0.94	2.019	7662
X-RAY DIFFRACTION	r_angle_other_deg	0.759	3	9595
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.884	5	737
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.956	20.878	205
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.655	15	767
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.581	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	839
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.022	6348
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1171
X-RAY DIFFRACTION	r_mcbond_it	0.666	2	3704
X-RAY DIFFRACTION	r_mcbond_other	0.094	2	1498
X-RAY DIFFRACTION	r_mcangle_it	1.269	3	5866
X-RAY DIFFRACTION	r_scbond_it	1.893	4	1904
X-RAY DIFFRACTION	r_scangle_it	3.396	6	1796

LS refinement shell

Resolution: 2.9→2.976 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.371	56	-
R_work	0.341	1037	-
all	-	1093	-
obs	-	-	43.81 %

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	1.8956	-0.4552	0.045	5.7786	-0.9337	0.3947	0.2039	-0.277	0.2135	0.263	-0.2374	-0.3938	0.0488	-0.0366	0.0335	0.3125	-0.0512	0.0887	0.1974	0.0002	0.0767	-56.6766	-3.0436	26.7233
2	1.4295	-0.4296	1.7604	2.8021	-2.0511	3.0002	-0.177	0.0755	0.1143	-0.281	-0.0936	-0.2867	-0.0229	0.1331	0.2707	0.354	0.0401	0.1183	0.1017	-0.0073	0.0733	-61.5121	17.831	6.4902
3	7.7467	-1.6655	-2.6222	2.8283	-0.9755	2.9918	-0.6397	1.8698	-0.7569	0.0067	0.1652	-0.248	0.1265	-0.9642	0.4746	0.2155	-0.2057	0.1743	0.8048	-0.2695	0.1282	-88.4106	35.3724	38.7097

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 209
2	X-RAY DIFFRACTION	2	A	210 - 493
3	X-RAY DIFFRACTION	3	B	221 - 493

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