PDB-3eit: the 2.6 angstrom crystal structure of CHBP, the Cif Homologue fro...

ID or keywords:

Entry

Database: PDB / ID: 3eit

Title

the 2.6 angstrom crystal structure of CHBP, the Cif Homologue from Burkholderia pseudomallei

Components

Putative ATP/GTP binding protein

Keywords

UNKNOWN FUNCTION / papain-like fold / apain superfamily / hydrolytic enzyme

Function / homology

Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase activity / protein-glutamine glutaminase / toxin activity / host cell nucleus / extracellular region / Protein-glutamine deamidase Cif

Function and homology information

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.56 Å

Authors

Yao, Q. / Zhu, Y. / Shao, F.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle
Authors: Yao, Q. / Cui, J. / Zhu, Y. / Wang, G. / Hu, L. / Long, C. / Cao, R. / Liu, X. / Huang, N. / Chen, S. / Liu, L. / Shao, F.

History

Deposition	Sep 17, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jul 20, 2011	Group: Refinement description
Revision 1.3	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3eit.cif.gz	103.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3eit.ent.gz	86.6 KB	Display	PDB format
PDBx/mmJSON format	3eit.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3eit_validation.pdf.gz	441.6 KB	Display	wwPDB validaton report
Full document	3eit_full_validation.pdf.gz	445.7 KB	Display
Data in XML	3eit_validation.xml.gz	19.3 KB	Display
Data in CIF	3eit_validation.cif.gz	26.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/3eit ftp://data.pdbj.org/pub/pdb/validation_reports/ei/3eit	HTTPS FTP

-
Related structure data

Related structure data	3eirC C: citing same article (ref.)
Similar structure data	3eir-1 1icf-2 5ia4-d 5tiu-d 5tr6-d 4i0t-d 5uab-d 4fyo-d 3eay-d 4zp5-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1)

Deposited unit

A: Putative ATP/GTP binding protein

B: Putative ATP/GTP binding protein

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

1

A: Putative ATP/GTP binding protein

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

2

B: Putative ATP/GTP binding protein

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

Unit cell

Length a, b, c (Å)	54.362, 78.003, 115.037
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative ATP/GTP binding protein / the EPEC effector Cif Homologue Mass: 31589.811 Da / Num. of mol.: 2 / Fragment: residues 48-328 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: YP_111397 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q63KH5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative ATP/GTP binding protein / the EPEC effector Cif Homologue

Mass: 31589.811 Da / Num. of mol.: 2 / Fragment: residues 48-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: YP_111397 / Plasmid: pGEX-6p-2 / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q63KH5

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.93 Å³/Da / Density % sol: 36.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97912 Å
Detector	Type: RIGAKU / Detector: IMAGE PLATE / Date: May 3, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97912 Å / Relative weight: 1
Reflection	Resolution: 2.56→50 Å / Num. all: 16433 / Num. obs: 16433 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / B_iso Wilson estimate: 51.5 Å² / R_merge(I) obs: 0.074 / R_sym value: 0.074 / Net I/σ(I): 26.9
Reflection shell	Resolution: 2.559→2.625 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.278 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1179 / R_sym value: 0.278 / % possible all: 75

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.006	data extraction
SERGUI		data collection
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.56→49.15 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.903 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.894 / SU ML: 0.247 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.267	1635	10.1 %	RANDOM
R_work	0.203	-	-	-
obs	0.21	16115	98.07 %	-

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: 58.74 Å² / B_iso mean: 30.502 Å² / B_iso min: 15.37 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.02 Å²	0 Å²	0 Å²
2-	-	-1.77 Å²	0 Å²
3-	-	-	-2.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.56→49.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3853	0	0	70	3923

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	3922
X-RAY DIFFRACTION	r_angle_refined_deg	1.11	1.969	5310
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.58	5	484
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.811	24.355	186
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.946	15	694
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.97	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	600
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2948
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	1699
X-RAY DIFFRACTION	r_nbtor_refined	0.297	0.2	2720
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	165
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.212	0.2	63
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.24	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.401	1.5	2485
X-RAY DIFFRACTION	r_mcangle_it	0.652	2	3916
X-RAY DIFFRACTION	r_scbond_it	1.283	3	1587
X-RAY DIFFRACTION	r_scangle_it	1.919	4.5	1394

LS refinement shell

Resolution: 2.559→2.625 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.39	87	-
R_work	0.265	804	-
all	-	891	-
obs	-	-	75.57 %

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	3.2977	-1.5386	0.253	5.5308	-1.413	2.7537	-0.0558	-0.0984	0.2448	0.1365	0.1019	0.0745	-0.056	-0.0586	-0.0461	0.0794	-0.0056	0.0132	0.0671	0.0088	0.0212	39.0661	34.5399	64.0379
2	4.6614	-1.4222	0.4337	8.6481	-1.914	6.8617	0.2995	0.1447	-0.1036	-0.2408	-0.0529	0.2177	0.216	-0.1487	-0.2465	0.0308	0.0421	0.0745	0.0697	0.0546	0.0946	21.6302	39.5226	49.9442
3	3.0196	-0.9439	-0.1787	2.747	0.172	4.2011	0.0143	0.0637	0.1779	-0.0075	0.0657	-0.2546	-0.3579	-0.009	-0.08	0.1442	0.0685	0.0444	-0.0017	0.0406	0.0369	44.7432	40.1613	56.7824
4	8.4475	-3.5701	-4.1923	8.3084	2.0605	3.4474	0.2208	0.1949	0.4872	0.2496	-0.3423	-0.3717	0.2979	0.1324	0.1215	-0.0193	-0.0173	0.0198	0.0538	0.0419	0.1473	63.8946	37.1862	55.7769
5	2.4896	-0.1493	0.8982	2.2456	-0.6426	2.3118	0.0422	0.075	0.0891	-0.1357	-0.1709	-0.0562	0.1361	0.1858	0.1287	0.1122	0.0587	0.0206	0.0534	0.0094	0.0505	49.4501	28.7886	54.4754
6	4.4178	-3.3311	0.1149	4.2101	2.3396	3.4691	0.149	0.6437	-0.016	-0.3999	-0.2526	-0.8757	-0.2981	0.02	0.1036	0.2287	0.0606	0.1139	0.016	-0.0396	0.1458	58.624	24.4573	50.679
7	2.6356	-0.9446	0.0225	3.9414	0.4123	1.9622	0.0766	0.5409	-0.1555	-0.662	-0.1379	-0.0223	0.0364	0.1636	0.0613	0.1251	0.0034	-0.015	0.0334	0.0415	-0.0263	52.6986	26.0919	50.0159
8	19.9181	-1.6263	-8.9989	9.7321	-11.3497	19.2786	0.435	-0.9308	0.6723	2.1256	-0.3085	0.1661	-0.7779	-0.2601	-0.1265	0.426	0.0687	0.0088	0.0872	-0.0805	0.0257	37.6125	36.9913	70.2708
9	2.9211	-0.3321	1.016	5.4818	-2.796	3.7365	-0.1014	-0.1248	-0.0284	-0.0771	0.1275	0.05	0.133	-0.1	-0.0261	0.2364	0.0246	0.0077	0.0445	-0.0137	-0.0485	36.8273	42.4579	29.1226
10	2.9986	0.1783	-0.655	6.3269	-2.516	5.8231	-0.0547	0.1434	-0.0474	-0.3374	0.0109	0.181	-0.0271	-0.2365	0.0438	0.1489	0.0283	-0.0566	0.0045	-0.0162	0.0357	32.9336	24.2227	40.3415
11	3.0609	0.111	-1.0651	4.7012	0.5354	6.9136	0.0683	-0.2971	0.0552	0.3146	-0.0465	-0.4995	-0.4018	0.8816	-0.0218	0.0848	0.0239	-0.0135	0.0381	0.0544	-0.0308	44.3012	47.7087	38.5836
12	2.4176	-1.1018	-1.2942	1.2992	1.9457	3.9444	-0.0186	-0.0609	0.423	-0.0435	0.118	-0.0752	-0.4999	0.3411	-0.0994	0.2376	-0.001	0.0133	0.0225	0.0284	0.0936	34.1202	59.6853	41.2713
13	14.913	0.238	-0.7658	4.1489	-1.3452	10.0751	-0.8503	-1.2381	-0.4136	0.4657	0.484	-0.0189	-0.2612	-0.0787	0.3663	0.3786	0.0411	0.027	0.017	-0.0218	0.0842	30.7993	56.4838	53.9843
14	5.1865	2.4428	-0.4874	4.7139	0.5424	5.9898	-0.0718	0.5755	0.1069	-0.448	0.2929	-0.3048	-0.0793	0.6485	-0.2211	0.1391	0.0615	0.0401	0.0352	0.1109	-0.0202	43.1045	49.1468	26.6277

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	79 - 119
2	X-RAY DIFFRACTION	2	A	120 - 151
3	X-RAY DIFFRACTION	3	A	152 - 181
4	X-RAY DIFFRACTION	4	A	182 - 197
5	X-RAY DIFFRACTION	5	A	198 - 249
6	X-RAY DIFFRACTION	6	A	250 - 272
7	X-RAY DIFFRACTION	7	A	273 - 318
8	X-RAY DIFFRACTION	8	A	319 - 327
9	X-RAY DIFFRACTION	9	B	80 - 119
10	X-RAY DIFFRACTION	10	B	120 - 151
11	X-RAY DIFFRACTION	11	B	152 - 185
12	X-RAY DIFFRACTION	12	B	186 - 291
13	X-RAY DIFFRACTION	13	B	292 - 306
14	X-RAY DIFFRACTION	14	B	307 - 327

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi