PDB-3k29: Structure of a putative YscO homolog CT670 from Chlamydia trachomatis

ID or keywords:

Entry

Database: PDB / ID: 3k29

Title

Structure of a putative YscO homolog CT670 from Chlamydia trachomatis

Components

Putative uncharacterized protein

Keywords

UNKNOWN FUNCTION / YscO / type III secretion apparatus / Chlamydia trachomatis / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases

Function / homology

YscO-like protein / YscO-like protein / Helix Hairpins - #1700 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Uncharacterized protein

Function and homology information

Biological species

Chlamydia trachomatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2 Å

Authors

Lam, R. / Singer, A. / Skarina, T. / Onopriyenko, O. / Bochkarev, A. / Brunzelle, J.S. / Edwards, A.M. / Anderson, W.F. / Chirgadze, N.Y. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: J.Bacteriol. / Year: 2010
Title: Structure and protein-protein interaction studies on Chlamydia trachomatis protein CT670 (YscO Homolog).
Authors: Lorenzini, E. / Singer, A. / Singh, B. / Lam, R. / Skarina, T. / Chirgadze, N.Y. / Savchenko, A. / Gupta, R.S.

History

Deposition	Sep 29, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 13, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3k29.cif.gz	46.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3k29.ent.gz	35.7 KB	Display	PDB format
PDBx/mmJSON format	3k29.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3k29_validation.pdf.gz	425.5 KB	Display	wwPDB validaton report
Full document	3k29_full_validation.pdf.gz	426.7 KB	Display
Data in XML	3k29_validation.xml.gz	8.2 KB	Display
Data in CIF	3k29_validation.cif.gz	10.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k2/3k29 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/3k29	HTTPS FTP

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Related structure data

Similar structure data	6ys4-2 7bji-2 5oi7-d 5hhe-2 5hhe-1 6ap0-d 4rfx-3 5k9l-2 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: IDP90225

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative uncharacterized protein

20.6 kDa, 1 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)	83.112, 23.194, 105.624
Angle α, β, γ (deg.)	90.000, 107.480, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-174- HOH

#1: Protein	Putative uncharacterized protein Mass: 20623.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: D/UW-3/CX / Gene: CT670, CT_670 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: O84677
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative uncharacterized protein

Mass: 20623.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chlamydia trachomatis (bacteria) / Strain: D/UW-3/CX / Gene: CT670, CT_670 / Plasmid: p15TvLic / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: O84677

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.35 Å³/Da / Density % sol: 47.75 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M ammonium dihydrogen phosphate, 20% PEG3350, 1% PEG4000, 1mM magnesium sulfate, and 25mM MES pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97921,0.97942

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2008 / Details: Be Lenses/Diamond Laue Mono

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97921	1
2	0.97942	1

Reflection

Redundancy: 6.1 % / Av σ(I) over netI: 25.76 / Number: 68202 / R_merge(I) obs: 0.073 / Χ²: 1.9 / D res high: 2.03 Å / D res low: 50 Å / Num. obs: 11202 / % possible obs: 85.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.37	50	98.6	1	0.065	4.967	6.5
3.47	4.37	99.9	1	0.054	2.167	6.9
3.03	3.47	100	1	0.059	1.603	7.1
2.76	3.03	100	1	0.089	1.387	7.1
2.56	2.76	99.5	1	0.138	1.272	6.7
2.41	2.56	97.6	1	0.168	1.182	5.8
2.29	2.41	89.7	1	0.207	1.088	5.1
2.19	2.29	74.7	1	0.23	1.125	4.7
2.1	2.19	54.2	1	0.286	1.101	4.6
2.03	2.1	42.6	1	0.296	1.034	4

Reflection

Resolution: 2→50 Å / Num. obs: 13438 / % possible obs: 99 % / Redundancy: 5.9 % / R_merge(I) obs: 0.067 / Χ²: 1.412 / Net I/σ(I): 14.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2-2.07	4.6	0.191	1231	0.787	1	91.6
2.07-2.15	5.3	0.166	1323	0.849	1	98.9
2.15-2.25	5.7	0.135	1321	0.962	1	99.8
2.25-2.37	6	0.113	1343	1.062	1	100
2.37-2.52	6	0.092	1339	1.158	1	99.9
2.52-2.71	6.3	0.081	1342	1.238	1	100
2.71-2.99	6.2	0.075	1352	1.282	1	100
2.99-3.42	6.3	0.063	1362	1.279	1	99.9
3.42-4.31	6.2	0.052	1380	1.729	1	100
4.31-50	5.8	0.066	1445	3.359	1	99.7

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Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	2.15	33.54	0	0	8715	1284
ISO_2	2.15	33.54	0.542	0.467	8600	1283
ANO_1	2.15	33.54	1.483	0	8130	0
ANO_2	2.15	33.54	1.788	0	8473	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	9.26-33.54	0	0	90	67
ISO_1	6.68-9.26	0	0	186	72
ISO_1	5.49-6.68	0	0	235	70
ISO_1	4.77-5.49	0	0	300	71
ISO_1	4.27-4.77	0	0	347	69
ISO_1	3.91-4.27	0	0	365	70
ISO_1	3.62-3.91	0	0	420	72
ISO_1	3.39-3.62	0	0	434	74
ISO_1	3.2-3.39	0	0	502	71
ISO_1	3.03-3.2	0	0	494	68
ISO_1	2.89-3.03	0	0	512	74
ISO_1	2.77-2.89	0	0	575	72
ISO_1	2.66-2.77	0	0	587	61
ISO_1	2.57-2.66	0	0	575	67
ISO_1	2.48-2.57	0	0	604	53
ISO_1	2.4-2.48	0	0	573	65
ISO_1	2.33-2.4	0	0	563	52
ISO_1	2.27-2.33	0	0	509	50
ISO_1	2.21-2.27	0	0	460	44
ISO_1	2.15-2.21	0	0	384	42
ANO_1	9.26-33.54	2.405	0	84	0
ANO_1	6.68-9.26	3.608	0	186	0
ANO_1	5.49-6.68	4	0	230	0
ANO_1	4.77-5.49	3.097	0	297	0
ANO_1	4.27-4.77	2.788	0	347	0
ANO_1	3.91-4.27	2.392	0	364	0
ANO_1	3.62-3.91	2.242	0	419	0
ANO_1	3.39-3.62	1.76	0	434	0
ANO_1	3.2-3.39	1.52	0	501	0
ANO_1	3.03-3.2	1.276	0	494	0
ANO_1	2.89-3.03	1.063	0	511	0
ANO_1	2.77-2.89	0.781	0	575	0
ANO_1	2.66-2.77	0.681	0	569	0
ANO_1	2.57-2.66	0.66	0	542	0
ANO_1	2.48-2.57	0.508	0	550	0
ANO_1	2.4-2.48	0.484	0	495	0
ANO_1	2.33-2.4	0.406	0	472	0
ANO_1	2.27-2.33	0.405	0	411	0
ANO_1	2.21-2.27	0.36	0	345	0
ANO_1	2.15-2.21	0.386	0	304	0
ISO_2	9.26-33.54	0.505	0.416	85	67
ISO_2	6.68-9.26	1.239	1.276	186	72
ISO_2	5.49-6.68	1.596	1.054	235	70
ISO_2	4.77-5.49	1.331	0.788	300	71
ISO_2	4.27-4.77	1.091	0.75	347	69
ISO_2	3.91-4.27	0.938	0.549	365	70
ISO_2	3.62-3.91	0.895	0.47	420	72
ISO_2	3.39-3.62	0.725	0.575	434	74
ISO_2	3.2-3.39	0.709	0.445	502	71
ISO_2	3.03-3.2	0.586	0.451	494	68
ISO_2	2.89-3.03	0.513	0.366	512	74
ISO_2	2.77-2.89	0.418	0.204	575	72
ISO_2	2.66-2.77	0.335	0.193	587	61
ISO_2	2.57-2.66	0.297	0.136	574	67
ISO_2	2.48-2.57	0.227	0.158	598	53
ISO_2	2.4-2.48	0.179	0.122	566	65
ISO_2	2.33-2.4	0.155	0.115	547	52
ISO_2	2.27-2.33	0.144	0.129	488	50
ISO_2	2.21-2.27	0.128	0.101	433	44
ISO_2	2.15-2.21	0.125	0.104	352	41
ANO_2	9.26-33.54	3.164	0	81	0
ANO_2	6.68-9.26	4.582	0	186	0
ANO_2	5.49-6.68	6.28	0	235	0
ANO_2	4.77-5.49	4.699	0	300	0
ANO_2	4.27-4.77	3.718	0	347	0
ANO_2	3.91-4.27	3.395	0	365	0
ANO_2	3.62-3.91	3.124	0	420	0
ANO_2	3.39-3.62	2.553	0	434	0
ANO_2	3.2-3.39	2.216	0	502	0
ANO_2	3.03-3.2	1.788	0	494	0
ANO_2	2.89-3.03	1.629	0	512	0
ANO_2	2.77-2.89	1.205	0	575	0
ANO_2	2.66-2.77	0.923	0	587	0
ANO_2	2.57-2.66	0.906	0	573	0
ANO_2	2.48-2.57	0.668	0	593	0
ANO_2	2.4-2.48	0.56	0	554	0
ANO_2	2.33-2.4	0.468	0	524	0
ANO_2	2.27-2.33	0.473	0	465	0
ANO_2	2.21-2.27	0.434	0	398	0
ANO_2	2.15-2.21	0.39	0	328	0

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 9998

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.2-100	61.6	0.875	503
4.89-6.2	58.4	0.876	506
4.26-4.89	55.1	0.885	506
3.85-4.26	56.3	0.883	505
3.58-3.85	54.5	0.869	501
3.36-3.58	58.9	0.858	508
3.19-3.36	61.3	0.825	510
3.05-3.19	64.6	0.832	504
2.92-3.05	64.2	0.802	505
2.82-2.92	64	0.804	502
2.73-2.82	64.2	0.756	503
2.65-2.73	71.3	0.764	503
2.57-2.65	74.7	0.731	509
2.5-2.57	76	0.748	512
2.44-2.5	74.9	0.754	501
2.38-2.44	75.5	0.719	502
2.32-2.38	78.3	0.744	513
2.26-2.32	80.6	0.67	514
2.15-2.26	83.5	0.664	891

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.5.0056	refinement
PDB_EXTRACT	3.005	data extraction
Blu-Ice	Max	data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2→27.41 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.91 / Occupancy max: 1 / Occupancy min: 0.24 / SU B: 11.632 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.196 / 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	0.285	653	4.9 %	RANDOM
R_work	0.24	-	-	-
obs	0.242	13431	98.24 %	-

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: 58.67 Å² / B_iso mean: 24.037 Å² / B_iso min: 10.81 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 2→27.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1373	0	0	51	1424

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1419
X-RAY DIFFRACTION	r_angle_refined_deg	1.535	1.993	1891
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.448	5	171
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.264	25.063	79
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.381	15	340
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.247	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	203
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1033
X-RAY DIFFRACTION	r_mcbond_it	0.839	1.5	824
X-RAY DIFFRACTION	r_mcangle_it	1.556	2	1334
X-RAY DIFFRACTION	r_scbond_it	3.002	3	595
X-RAY DIFFRACTION	r_scangle_it	5.008	4.5	552

LS refinement shell

Resolution: 1.993→2.044 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.328	41	-
R_work	0.277	739	-
all	-	780	-
obs	-	-	79.51 %

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	0.8192	0.3602	-0.606	1.375	-3.5726	16.6018	-0.0507	-0.0934	-0.0867	-0.2284	-0.2849	-0.2049	1.2131	0.7789	0.3356	0.2923	0.0433	-0.005	0.1724	0.0573	0.2505	11.6276	4.012	51.573
2	1.1142	-0.1692	0.2079	1.5968	-2.7426	10.6366	-0.1135	0.0002	-0.0821	-0.1502	-0.1006	-0.1486	0.6544	0.3331	0.2141	0.1353	-0.0117	0.0315	0.1359	0.031	0.177	12.7516	19.7392	3.1654
3	0.4067	-0.6248	2.4895	0.9599	-3.8247	15.239	-0.1598	-0.0655	-0.0245	0.2432	-0.0729	-0.1618	-0.5338	0.0654	0.2326	0.1425	-0.0181	0.0015	0.1727	0.0319	0.2222	10.2035	15.6404	35.3773
4	1.9424	-0.9151	2.4957	3.3483	-5.5256	16.5048	-0.1735	0.2136	0.1758	0.119	-0.2247	-0.0864	-0.8134	0.578	0.3981	0.1541	-0.0615	-0.0378	0.2269	0.0783	0.311	23.8258	-0.123	93.7137
5	1.3493	0.056	4.3457	1.7962	-1.8881	16.3809	-0.0168	-0.5466	-0.076	0.6139	-0.2984	-0.2649	0.3267	1.0151	0.3153	0.3061	-0.0162	-0.0301	0.4377	0.1289	0.4458	28.0621	-9.369	114.7082

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 37
2	X-RAY DIFFRACTION	2	A	38 - 73
3	X-RAY DIFFRACTION	3	A	74 - 131
4	X-RAY DIFFRACTION	4	A	132 - 156
5	X-RAY DIFFRACTION	5	A	157 - 162

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