PDB-3zzo: Crystal structure of the CG11501 protein in P212121 spacegroup

ID or keywords:

Entry

Database: PDB / ID: 3zzo

Title

Crystal structure of the CG11501 protein in P212121 spacegroup

Components

CG11501

Keywords

IMMUNE SYSTEM / IMMUNE RESPONSE

Function / homology

Function and homology information

immune system process / cytokine activity / response to bacterium / defense response to virus / extracellular space
Similarity search - Function

Biological species

DROSOPHILA MELANOGASTER (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.15 Å

Authors

Coste, F. / Roussel, A.

Citation

Journal: Plos One / Year: 2012
Title: Crystal Structure of Diedel, a Marker of the Immune Response of Drosophila Melanogaster.
Authors: Coste, F. / Kemp, C. / Bobezeau, V. / Hetru, C. / Kellenberger, C. / Imler, J.-L. / Roussel, A.

History

Deposition	Sep 2, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 11, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3zzo.cif.gz	53.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3zzo.ent.gz	42.7 KB	Display	PDB format
PDBx/mmJSON format	3zzo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3zzo_validation.pdf.gz	426.6 KB	Display	wwPDB validaton report
Full document	3zzo_full_validation.pdf.gz	426.6 KB	Display
Data in XML	3zzo_validation.xml.gz	7.7 KB	Display
Data in CIF	3zzo_validation.cif.gz	10.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzo ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzo	HTTPS FTP

-
Related structure data

Related structure data	3zzrC C: citing same article (ref.)
Similar structure data	3hjx-d 2vqh-1 2vqk-d 2vql-1 2ope-4 1n5h-d 4lw9-7 6cjz-d 2vqh-2 4yx2-1 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	#190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: CG11501

hetero molecules

10.7 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)	29.916, 44.576, 59.005
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CG11501 / RH38110P Mass: 10583.995 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PMT/V5-HIS A / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q9VAK8
#2: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE MUTATION S75P SEEN IN THE CRYSTAL STRUCTURE MIGHT BE DUE TO AN ERROR INTO THE SEQUENCE DATABASE

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.83 Å³/Da / Density % sol: 33 % / Description: NONE
Crystal grow	pH: 5.5 / Details: 50MM NA-ACETATE PH5.5, 200MM NASCN, 18-25% PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9834
Detector	Type: ADSC CCD / Detector: CCD / Date: Mar 25, 2008 / Details: TOROIDAL MIRROR
Radiation	Monochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9834 Å / Relative weight: 1
Reflection	Resolution: 1.15→19 Å / Num. obs: 28072 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / B_iso Wilson estimate: 11.8 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shell	Resolution: 1.15→1.21 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.26 / Mean I/σ(I) obs: 3.1 / % possible all: 97.6

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
SCALA		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SIRAS
Starting model: NONE

Resolution: 1.15→18 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.969 / SU B: 0.875 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.15129	1422	5.1 %	RANDOM
R_work	0.12892	-	-	-
obs	0.13006	26611	97.54 %	-

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: 12.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0 Å²	0 Å²
2-	-	-0.21 Å²	0 Å²
3-	-	-	0.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.15→18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	711	0	7	144	862

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	756
X-RAY DIFFRACTION	r_bond_other_d	0.018	0.02	521
X-RAY DIFFRACTION	r_angle_refined_deg	1.595	1.937	1023
X-RAY DIFFRACTION	r_angle_other_deg	1.325	3	1260
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.869	5	96
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.081	24.75	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.353	15	124
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.229	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.131	0.2	105
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	863
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	157
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.518	1.5	466
X-RAY DIFFRACTION	r_mcbond_other	0.644	1.5	195
X-RAY DIFFRACTION	r_mcangle_it	2.223	2	746
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.202	3	290
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.259	4.5	275
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	1.538	3	1277
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.15→1.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.229	95	-
R_work	0.201	1860	-
obs	-	-	94.81 %

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	0.8956	0.4099	-0.0871	0.1298	-0.0367	0.6149	0.0035	-0.0518	-0.0499	-0.0045	-0.0127	-0.017	0.0155	0.0346	0.0092	0.0488	0.0015	-0.0005	0.0633	0.0071	0.0417	15.354	19.632	19.029
2	0.7476	-0.1346	1.0714	0.1662	-0.1194	1.6236	0.0274	-0.0122	-0.041	-0.0101	-0.0046	0.0013	0.0317	-0.0175	-0.0229	0.0474	-0.0005	-0.0005	0.0566	0.0005	0.0391	2.094	16.943	8.38
3	0.7283	-0.1386	0.7828	0.0211	-0.1045	1.2497	-0.0276	0.0619	-0.007	-0.0034	-0.0083	0.0052	-0.0753	0.0645	0.036	0.0521	-0.0053	-0.0025	0.0601	0.0013	0.0348	2.034	23.658	-0.725
4	7.639	12.1698	7.5386	21.4926	11.5596	6.1591	0.3864	0.3859	-0.5587	0.3123	0.2243	-0.4889	0.4746	0.3124	-0.6107	0.1412	-0.0094	-0.077	0.084	-0.0378	0.0559	0.414	12.017	-1.778
5	0.9723	0.2748	0.4616	0.4621	0.4213	0.4149	-0.0006	0.0083	-0.0056	0.0041	0.0092	-0.0134	0.0051	0.009	-0.0085	0.0485	-0.0023	0.0024	0.0575	0.0026	0.0345	7.382	21.811	9.007
6	0.5415	0.0532	-0.032	0.0797	-0.021	0.1763	-0.0033	-0.0452	-0.0159	0.0041	0.0028	0.0076	0.0013	-0.0005	0.0005	0.0471	0.0008	0.0019	0.0603	0.0017	0.0371	21.779	23.774	16.734
7	1.3847	0.31	0.0586	0.0761	-0.0057	0.1916	0.0115	-0.0804	0.0278	-0.0013	-0.0041	0.006	-0.0042	-0.0052	-0.0074	0.0452	0.0014	0.0004	0.0614	-0.0047	0.0384	9.313	26.886	18.014
8	0.4412	-0.2433	0.2099	0.343	-0.0947	0.1458	-0.0049	0.0109	0.0174	-0.0053	-0.0177	-0.009	-0.005	0.0031	0.0226	0.0476	0.0004	-0.0003	0.0569	-0.0003	0.038	0.32	28.872	10.8
9	0.2677	-0.3492	0.3507	0.9584	-0.6245	1.0393	-0.0078	-0.0094	-0.0175	-0.0251	-0.0114	-0.0178	-0.031	-0.0318	0.0192	0.0504	0.0025	0.0022	0.0535	-0.0016	0.0335	-2.684	21.804	6.769
10	2.9223	-2.5642	1.5813	7.2552	-3.084	1.2961	-0.0422	0.067	0.0906	0.0985	-0.06	-0.2278	-0.0389	0.0312	0.1022	0.0463	-0.0017	0.0035	0.051	0.0023	0.0381	8.348	11.045	18.981

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 30
2	X-RAY DIFFRACTION	2	A	31 - 36
3	X-RAY DIFFRACTION	3	A	37 - 48
4	X-RAY DIFFRACTION	4	A	49 - 53
5	X-RAY DIFFRACTION	5	A	54 - 65
6	X-RAY DIFFRACTION	6	A	66 - 84
7	X-RAY DIFFRACTION	7	A	85 - 93
8	X-RAY DIFFRACTION	8	A	94 - 101
9	X-RAY DIFFRACTION	9	A	102 - 110
10	X-RAY DIFFRACTION	10	A	111 - 117

-
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://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