PDB-8dj2: Intramolecular ester bond-containing repeat domain from Chlamydia...

ID or keywords:

Entry

Database: PDB / ID: 8dj2

Title

Intramolecular ester bond-containing repeat domain from Chlamydia trachomatis adhesin

Components

Adhesin

Keywords

CELL ADHESION / adhesin repeat domain / intramolecular ester bond / Ig-like domain

Function / homology

Immunoglobulin-like - #3930 / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Chlamydia trachomatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Choksi, Z.N. / Young, P.G. / Squire, C.J.

Funding support

New Zealand, 1items

Citation

Journal: To Be Published
Title: Intramolecular ester bond-containing repeat domain from Chlamydia trachomatis adhesin
Authors: Choksi, Z.N. / Young, P.G. / Squire, C.J.

History

Deposition	Jun 29, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 2, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8dj2.cif.gz	168.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8dj2.ent.gz	102.3 KB	Display	PDB format
PDBx/mmJSON format	8dj2.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/dj/8dj2 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/8dj2	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Adhesin

B: Adhesin

hetero molecules

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

1

A: Adhesin

hetero molecules

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

2

B: Adhesin

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.050, 91.050, 88.752
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-1001- GOL

#1: Protein	Adhesin Mass: 15516.914 Da / Num. of mol.: 2 Fragment: intramolecular ester bond containing repeat domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Plasmid: pPROEXT-Hta / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.5 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 1.3 M sodium citrate, pH 6.3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 26, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 1.49→45.53 Å / Num. obs: 60739 / % possible obs: 99.7 % / Redundancy: 26.6 % / CC_1/2: 0.996 / Net I/σ(I): 11
Reflection shell	Resolution: 1.49→1.52 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2798 / CC_1/2: 0.294

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0349	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: alphafold prediction

Resolution: 1.5→19.945 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.962 / SU B: 7.078 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2189	895	1.489 %
R_work	0.1772	59227	-
all	0.178	-	-
obs	-	60122	99.922 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.591 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.782 Å²	0 Å²	0 Å²
2-	-	4.782 Å²	-0 Å²
3-	-	-	-9.563 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→19.945 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2050	0	21	277	2348

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	2153
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	1934
X-RAY DIFFRACTION	r_angle_refined_deg	1.006	1.634	2913
X-RAY DIFFRACTION	r_angle_other_deg	0.384	1.562	4501
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.741	5	302
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.907	10	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.088	10	305
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.858	10	82
X-RAY DIFFRACTION	r_chiral_restr	0.045	0.2	355
X-RAY DIFFRACTION	r_chiral_restr_other	0.056	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2500
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	388
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	337
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	1756
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	1028
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1144
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	220
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.31	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.173	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.116	0.2	22
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.234	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.725	3.177	1182
X-RAY DIFFRACTION	r_mcbond_other	3.726	3.174	1179
X-RAY DIFFRACTION	r_mcangle_it	4.604	4.769	1470
X-RAY DIFFRACTION	r_mcangle_other	4.603	4.77	1471
X-RAY DIFFRACTION	r_scbond_it	4.146	3.569	971
X-RAY DIFFRACTION	r_scbond_other	4.145	3.569	972
X-RAY DIFFRACTION	r_scangle_it	5.091	5.176	1437
X-RAY DIFFRACTION	r_scangle_other	5.09	5.177	1438
X-RAY DIFFRACTION	r_lrange_it	7.338	49.35	2295
X-RAY DIFFRACTION	r_lrange_other	7.088	45.904	2235
X-RAY DIFFRACTION	r_rigid_bond_restr	11.691	3	4087

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.5-1.539	0.368	82	0.339	4255	0.339	4343	0.944	0.95	99.8618	0.326
1.539-1.581	0.266	57	0.314	4201	0.314	4258	0.982	0.965	100	0.292
1.581-1.626	0.333	46	0.281	4092	0.281	4139	0.944	0.974	99.9758	0.255
1.626-1.676	0.256	74	0.264	3946	0.264	4020	0.977	0.979	100	0.234
1.676-1.73	0.321	76	0.237	3826	0.238	3902	0.945	0.983	100	0.205
1.73-1.791	0.27	47	0.223	3755	0.223	3802	0.975	0.987	100	0.188
1.791-1.858	0.23	47	0.204	3596	0.204	3643	0.958	0.988	100	0.171
1.858-1.933	0.252	75	0.192	3457	0.193	3532	0.978	0.99	100	0.167
1.933-2.018	0.225	38	0.178	3361	0.178	3399	0.992	0.991	100	0.161
2.018-2.115	0.171	51	0.174	3194	0.174	3245	0.978	0.991	100	0.166
2.115-2.228	0.239	44	0.173	3035	0.174	3079	0.977	0.989	100	0.172
2.228-2.362	0.241	48	0.168	2888	0.169	2936	0.979	0.989	100	0.174
2.362-2.522	0.212	26	0.182	2759	0.182	2785	0.981	0.987	100	0.194
2.522-2.721	0.281	35	0.185	2540	0.187	2575	0.956	0.984	100	0.208
2.721-2.975	0.229	33	0.173	2370	0.174	2403	0.979	0.984	100	0.205
2.975-3.317	0.176	32	0.169	2172	0.169	2204	0.99	0.984	100	0.202
3.317-3.812	0.245	20	0.148	1934	0.149	1954	0.961	0.988	100	0.183
3.812-4.627	0.171	28	0.13	1659	0.131	1687	0.982	0.99	100	0.175
4.627-6.374	0.165	27	0.16	1327	0.16	1354	0.988	0.988	100	0.219
6.374-19.945	0.219	9	0.197	860	0.197	869	0.97	0.968	100	0.265

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