PDB-2hr2: Crystal structure of a tpr-like protein (ct2138) from chlorobium ...

ID or keywords:

Entry

Database: PDB / ID: 2hr2

Title

Crystal structure of a tpr-like protein (ct2138) from chlorobium tepidum tls at 2.54 A resolution

Components

Hypothetical protein

Keywords

UNKNOWN FUNCTION / Alpha-alpha superhelix fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Domain of Unknown Function DUF3856 / Domain of Unknown Function (DUF3856) / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / DUF3856 domain-containing protein

Function and homology information

Biological species

Chlorobium tepidum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.54 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of hypothetical protein (NP_663012.1) from Chlorobium tepidum TLS at 2.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jul 19, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Jan 25, 2023	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...

Remark 300

BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2hr2.cif.gz	180.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2hr2.ent.gz	150.4 KB	Display	PDB format
PDBx/mmJSON format	2hr2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2hr2_validation.pdf.gz	485.2 KB	Display	wwPDB validaton report
Full document	2hr2_full_validation.pdf.gz	492 KB	Display
Data in XML	2hr2_validation.xml.gz	32.9 KB	Display
Data in CIF	2hr2_validation.cif.gz	44.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/2hr2 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hr2	HTTPS FTP

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Related structure data

Similar structure data	5g5d-1 3ask-4 3hva-2 4zvh-2 2xh3-1 6k01-d 2jhz-2 6k03-d 1qvy-2 3bqa-1 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) 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: 366651

Similar structure data

Other databases

TargetDB: 366651

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein

B: Hypothetical protein

C: Hypothetical protein

D: Hypothetical protein

E: Hypothetical protein

F: Hypothetical protein

hetero molecules

108 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hypothetical protein

hetero molecules

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

2

B: Hypothetical protein

hetero molecules

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

3

C: Hypothetical protein

hetero molecules

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

4

D: Hypothetical protein

hetero molecules

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

5

E: Hypothetical protein

hetero molecules

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

6

F: Hypothetical protein

hetero molecules

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

7

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	89.090, 91.280, 176.170
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	4	A	A	2 - 5	3 - 6
2	1	MSE	LYS	4	B	B	1 - 5	2 - 6
3	1	MSE	LYS	4	C	C	1 - 5	2 - 6
4	1	MSE	LYS	4	D	D	1 - 5	2 - 6
5	1	MSE	LYS	4	E	E	1 - 5	2 - 6
6	1	MSE	LYS	4	F	F	1 - 5	2 - 6
1	2	GLU	ILE	2	A	A	6 - 152	7 - 153
2	2	GLU	ILE	2	B	B	6 - 152	7 - 153
3	2	GLU	ILE	2	C	C	6 - 152	7 - 153
4	2	GLU	ILE	2	D	D	6 - 152	7 - 153
5	2	GLU	ILE	2	E	E	6 - 152	7 - 153
6	2	GLU	ILE	2	F	F	6 - 152	7 - 153
1	3	ALA	ALA	4	A	A	153 - 157	154 - 158
2	3	ALA	ALA	4	B	B	153 - 157	154 - 158
3	3	ALA	ALA	4	C	C	153 - 157	154 - 158
4	3	ALA	ALA	4	D	D	153 - 157	154 - 158
5	3	ALA	ALA	4	E	E	153 - 157	154 - 158
6	3	ALA	GLY	4	F	F	153 - 156	154 - 157

NCS ensembles :

ID
1
2
3

#1: Protein	Hypothetical protein Mass: 17762.000 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobium tepidum (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS / Gene: NP_663012.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KAL8
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.54 Å³/Da / Density % sol: 64.94 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5 Details: 25.0% Glycerol, 0.6M KH2PO4, 0.6M NaH2PO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.91837, 0.97936, 0.97920

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 17, 2006 / Details: Flat collimating mirror, toroid focusing mirror

Radiation

Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91837	1
2	0.97936	1
3	0.9792	1

Reflection

Resolution: 2.54→29.696 Å / Num. obs: 47660 / % possible obs: 90.9 % / Redundancy: 2.18 % / B_iso Wilson estimate: 57.6 Å² / R_merge(I) obs: 0.073 / Net I/σ(I): 8.08

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique all	% possible all
2.54-2.63		2.15	0.563	1.8	16175	7287	80.6
2.63-2.74			0.438	2.2	17679	7959	83.5
2.74-2.86			0.349	2.7	16989	7687	86.8
2.86-3.01			0.266	3.4	17870	8104	89.6
3.01-3.2			0.197	4.5	18774	8520	91.8
3.2-3.44			0.117	6.8	18472	8379	93.8
3.44-3.79			0.073	9.7	19508	8919	95.8
3.79-4.33			0.05	13.3	19170	8726	96.2
	4.33		0.044	15	19464	8845	96.2

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
MolProbity	3beta29	model building
SHARP		phasing
REFMAC	5.2.0005	refinement
XSCALE		data scaling
PDB_EXTRACT	2	data extraction
XDS		data reduction
SHELXD		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.54→29.696 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.94 / SU B: 20.249 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.24
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.232	2415	5.1 %	RANDOM
R_work	0.204	-	-	-
obs	0.205	47611	98.87 %	-

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 mean: 58.893 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.19 Å²	0 Å²	0 Å²
2-	-	0.88 Å²	0 Å²
3-	-	-	1.31 Å²

Refinement step

Cycle: LAST / Resolution: 2.54→29.696 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7055	0	81	88	7224

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	7259
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	6650
X-RAY DIFFRACTION	r_angle_refined_deg	1.171	1.964	9763
X-RAY DIFFRACTION	r_angle_other_deg	0.857	3	15327
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.292	5	938
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.423	23.769	337
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.041	15	1176
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.606	15	57
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1037
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	8287
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1500
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.3	1637
X-RAY DIFFRACTION	r_nbd_other	0.137	0.3	6070
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.5	3537
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.5	4026
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.5	203
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.004	0.5	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.138	0.3	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.151	0.3	54
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.152	0.5	4
X-RAY DIFFRACTION	r_mcbond_it	0.888	3	4879
X-RAY DIFFRACTION	r_mcbond_other	0.287	3	1942
X-RAY DIFFRACTION	r_mcangle_it	0.984	5	7280
X-RAY DIFFRACTION	r_scbond_it	2.673	8	2772
X-RAY DIFFRACTION	r_scangle_it	3.8	11	2481

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	49	MEDIUM POSITIONAL	0.75	0.5
1	2	B	49	MEDIUM POSITIONAL	0.3	0.5
1	3	C	49	MEDIUM POSITIONAL	0.23	0.5
1	4	D	49	MEDIUM POSITIONAL	0.27	0.5
1	5	E	49	MEDIUM POSITIONAL	0.33	0.5
1	6	F	49	MEDIUM POSITIONAL	0.3	0.5
1	1	A	49	MEDIUM THERMAL	0.42	2
1	2	B	49	MEDIUM THERMAL	0.16	2
1	3	C	49	MEDIUM THERMAL	0.19	2
1	4	D	49	MEDIUM THERMAL	0.23	2
1	5	E	49	MEDIUM THERMAL	0.18	2
1	6	F	49	MEDIUM THERMAL	0.31	2
2	1	A	862	TIGHT POSITIONAL	0.02	0.05
2	2	B	862	TIGHT POSITIONAL	0.02	0.05
2	3	C	862	TIGHT POSITIONAL	0.02	0.05
2	4	D	862	TIGHT POSITIONAL	0.02	0.05
2	5	E	862	TIGHT POSITIONAL	0.02	0.05
2	6	F	862	TIGHT POSITIONAL	0.02	0.05
2	1	A	1201	MEDIUM POSITIONAL	0.34	0.5
2	2	B	1201	MEDIUM POSITIONAL	0.4	0.5
2	3	C	1201	MEDIUM POSITIONAL	0.38	0.5
2	4	D	1201	MEDIUM POSITIONAL	0.45	0.5
2	5	E	1201	MEDIUM POSITIONAL	0.39	0.5
2	6	F	1201	MEDIUM POSITIONAL	0.29	0.5
2	1	A	862	TIGHT THERMAL	0.03	0.5
2	2	B	862	TIGHT THERMAL	0.03	0.5
2	3	C	862	TIGHT THERMAL	0.03	0.5
2	4	D	862	TIGHT THERMAL	0.04	0.5
2	5	E	862	TIGHT THERMAL	0.03	0.5
2	6	F	862	TIGHT THERMAL	0.03	0.5
2	1	A	1201	MEDIUM THERMAL	0.27	2
2	2	B	1201	MEDIUM THERMAL	0.26	2
2	3	C	1201	MEDIUM THERMAL	0.3	2
2	4	D	1201	MEDIUM THERMAL	0.32	2
2	5	E	1201	MEDIUM THERMAL	0.29	2
2	6	F	1201	MEDIUM THERMAL	0.26	2
3	1	A	51	MEDIUM POSITIONAL	0.22	0.5
3	2	B	51	MEDIUM POSITIONAL	0.28	0.5
3	3	C	51	MEDIUM POSITIONAL	0.24	0.5
3	4	D	51	MEDIUM POSITIONAL	0.53	0.5
3	5	E	51	MEDIUM POSITIONAL	0.49	0.5
3	6	F	51	MEDIUM POSITIONAL	0.36	0.5
3	1	A	51	MEDIUM THERMAL	0.13	2
3	2	B	51	MEDIUM THERMAL	0.27	2
3	3	C	51	MEDIUM THERMAL	0.18	2
3	4	D	51	MEDIUM THERMAL	0.36	2
3	5	E	51	MEDIUM THERMAL	0.37	2
3	6	F	51	MEDIUM THERMAL	0.35	2

LS refinement shell

Resolution: 2.54→2.606 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.358	195	-
R_work	0.329	3285	-
obs	-	3480	99.83 %

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	4.5855	0.5922	-2.0524	3.4791	-1.3184	5.1686	0.3476	-0.5349	0.7449	0.2904	-0.1625	-0.1227	-0.7296	0.2442	-0.185	0.0235	-0.1029	0.0035	-0.0595	-0.1566	-0.0723	90.44	50.918	84.319
2	5.5644	1.6776	0.4369	3.0561	-0.5752	2.6954	-0.0391	-0.0429	0.4703	-0.0326	0.1002	0.2427	-0.3895	-0.1962	-0.0611	0.0895	0.1221	0.1896	-0.2003	0.168	-0.1033	76.815	57.115	54.539
3	3.7149	-0.9178	1.1117	2.7344	-1.0562	6.1055	0.0741	-0.3835	0.3511	0.1918	0.0193	0.1783	-0.6202	-0.364	-0.0935	-0.2083	0.0352	0.1216	-0.1793	0.0225	-0.1246	58.276	43.093	78.638
4	5.9233	-0.0791	0.6001	1.9758	-0.3685	2.5336	0.006	-0.0871	-0.4135	-0.1194	0.0021	0.0162	0.1447	-0.1383	-0.0082	-0.2213	0.0242	-0.0259	-0.1768	0.0962	-0.1787	85.706	21.082	82.116
5	2.7727	0.4166	-0.7175	2.7441	-1.1606	5.4555	0.0458	0.2626	-0.3779	-0.3512	-0.0222	0.0724	0.3811	-0.1174	-0.0236	-0.1825	0.0242	-0.0492	-0.1647	-0.0855	-0.147	65.051	23.643	56.044
6	5.2082	0.3538	1.8615	2.0714	0.4337	5.0642	0.1211	0.3773	-0.2441	-0.196	-0.0294	-0.3298	0.1114	0.4433	-0.0916	-0.1101	0.0572	0.1664	-0.1675	-0.0148	-0.1844	96.593	34.05	53.433

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	2 - 157	3 - 158
2	2	B	B	1 - 157	2 - 158
3	3	C	C	1 - 157	2 - 158
4	4	D	D	1 - 157	2 - 158
5	5	E	E	1 - 157	2 - 158
6	6	F	F	1 - 156	2 - 157

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