PDB-2ii2: Crystal Structure of Alpha-11 Giardin

ID or keywords:

Entry

Database: PDB / ID: 2ii2

Title

Crystal Structure of Alpha-11 Giardin

Components

Alpha-11 giardin

Keywords

METAL BINDING PROTEIN / Helix-Turn-Helix

Function / homology

Function and homology information

calcium-dependent phospholipid binding / cytoskeleton organization / microtubule / calcium ion binding
Similarity search - Function

Biological species

Giardia intestinalis (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.1 Å

Authors

Pathuri, P. / Nguyen, E.T. / Luecke, H.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Apo and Calcium-bound Crystal Structures of Alpha-11 Giardin, an Unusual Annexin from Giardia lamblia
Authors: Pathuri, P. / Nguyen, E.T. / Svard, S.G. / Luecke, H.

History

Deposition	Sep 27, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 17, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2ii2.cif.gz	161.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2ii2.ent.gz	125.2 KB	Display	PDB format
PDBx/mmJSON format	2ii2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2ii2_validation.pdf.gz	427.2 KB	Display	wwPDB validaton report
Full document	2ii2_full_validation.pdf.gz	428.6 KB	Display
Data in XML	2ii2_validation.xml.gz	18.9 KB	Display
Data in CIF	2ii2_validation.cif.gz	31.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ii/2ii2 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/2ii2	HTTPS FTP

-
Related structure data

Related structure data	2iicC C: citing same article (ref.)
Similar structure data	4evh-d 4evf-d 3f9u-d 3chj-d 4lgt-1 1rzn-d 3dh3-1 1x11-3 1hg5-d 2q4c-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alpha-11 giardin

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	45.951, 60.954, 119.909
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Alpha-11 giardin Mass: 35252.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia intestinalis (eukaryote) / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q4VPP2
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.7 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 200mM Lithium Sulfate, 100mM MES pH 6.0, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction

ID	Crystal-ID
1	1
2	1
3	1

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-1 / Wavelength: 0.979,0.905

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2006

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	0.905	1

Reflection

D res high: 1.92 Å / D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
5.3	1	12.1	256287	0.073	0.84	48518	98.6
6	2	10.4	291574	0.095	2.09	48700	98.6
5.2	3	10.8	260134	0.075	0.81	49602	99.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy	Rejects
5.21	50	99.4	1	0.034	1.18	5.6	4836
4.14	5.21	99.8	1	0.039	1.112	5.2	3755
3.61	4.14	100	1	0.048	1.026	5.5	431
3.28	3.61	100	1	0.053	0.969	5.5	53
3.05	3.28	100	1	0.06	0.893	5.5	1
2.87	3.05	99.9	1	0.069	0.84	5.4	2
2.72	2.87	99.9	1	0.077	0.851	5.4	8
2.61	2.72	99.7	1	0.087	0.837	5.3	4
2.51	2.61	99.5	1	0.094	0.8	5.4	2
2.42	2.51	99.8	1	0.104	0.812	5.3
2.34	2.42	99.1	1	0.112	0.794	5.3
2.28	2.34	99.7	1	0.123	0.778	5.3
2.22	2.28	98.8	1	0.136	0.775	5.2
2.16	2.22	99.8	1	0.143	0.761	5.2
2.11	2.16	98.4	1	0.154	0.756	5.2
2.07	2.11	99.6	1	0.176	0.741	5.2
2.03	2.07	97.5	1	0.206	0.722	5.1
1.99	2.03	99	1	0.238	0.71	5.2
1.95	1.99	97.3	1	0.276	0.675	5.1
1.92	1.95	85.5	1	0.304	0.708	4.7
5.21	50	99.6	2	0.057	2.553	6.2	4836
4.14	5.21	100	2	0.059	2.772	5.8	3755
3.61	4.14	100	2	0.065	2.902	5.9	431
3.28	3.61	100	2	0.073	2.887	6	53
3.05	3.28	100	2	0.081	2.546	6.1	1
2.87	3.05	99.9	2	0.092	2.401	6.1	2
2.72	2.87	99.8	2	0.101	2.287	6.1	8
2.61	2.72	99.6	2	0.111	2.217	6.1	4
2.51	2.61	99.6	2	0.12	2.206	6.1	2
2.42	2.51	100	2	0.128	2.049	6
2.34	2.42	99.4	2	0.141	2.049	6.1
2.28	2.34	100	2	0.153	1.975	6.1
2.22	2.28	99.1	2	0.162	1.918	6
2.16	2.22	100	2	0.175	1.84	6
2.11	2.16	98.8	2	0.186	1.723	6
2.07	2.11	100	2	0.212	1.653	6
2.03	2.07	98.2	2	0.241	1.537	6
1.99	2.03	100	2	0.267	1.395	5.9
1.95	1.99	97.9	2	0.317	1.294	5.9
1.92	1.95	80	2	0.334	1.304	5.3
5.21	50	99.5	3	0.032	1.106	5.7	4836
4.14	5.21	99.4	3	0.035	1.082	5.3	3755
3.61	4.14	100	3	0.043	1.05	5.4	431
3.28	3.61	100	3	0.052	0.993	5.5	53
3.05	3.28	99.9	3	0.059	0.848	5.5	1
2.87	3.05	100	3	0.068	0.815	5.4	2
2.72	2.87	100	3	0.078	0.783	5.3	8
2.61	2.72	99.9	3	0.087	0.77	5.3	4
2.51	2.61	99.6	3	0.095	0.745	5.3	2
2.42	2.51	99.8	3	0.108	0.771	5.2
2.34	2.42	99.4	3	0.118	0.751	5.2
2.28	2.34	99.4	3	0.128	0.733	5.2
2.22	2.28	99.1	3	0.141	0.742	5.1
2.16	2.22	99.3	3	0.156	0.719	5.1
2.11	2.16	98.8	3	0.165	0.711	5.1
2.07	2.11	99.6	3	0.204	0.727	5.1
2.03	2.07	98.1	3	0.232	0.695	5.1
1.99	2.03	98.3	3	0.263	0.707	5.1
1.95	1.99	97	3	0.318	0.671	5
1.92	1.95	98.2	3	0.343	0.677	4.9

Reflection

Resolution: 1.1→42.74 Å / Num. obs: 133460 / % possible obs: 97.2 % / Redundancy: 9.01 % / R_merge(I) obs: 0.121 / Χ²: 0.74 / Net I/σ(I): 6.4 / Scaling rejects: 9092

Reflection shell

Resolution: 1.1→1.14 Å / Redundancy: 5.98 % / R_merge(I) obs: 0.482 / Mean I/σ(I) obs: 2 / Num. measured all: 76436 / Num. unique all: 12772 / Χ²: 0.43 / % possible all: 94.2

-
Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9793	8.83	-9.67
1	3 wavelength	2	0.905	4.68	-2.58
1	3 wavelength	3	0.9795	3.01	-11.1

Phasing dm

FOM : 0.86 / FOM acentric: 0.86 / FOM centric: 0.83 / Reflection: 12017 / Reflection acentric: 10168 / Reflection centric: 1849

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
7.1-34.838	0.96	0.97	0.94	582	367	215
4.5-7.1	0.94	0.95	0.9	1659	1298	361
3.6-4.5	0.93	0.94	0.87	2033	1699	334
3.1-3.6	0.9	0.91	0.83	2014	1732	282
2.7-3.1	0.82	0.82	0.78	3546	3124	422
2.5-2.7	0.74	0.75	0.66	2183	1948	235

-
Processing

Software

Name	Version	Classification
d*TREK	9.2L	data scaling
SOLVE	2.09	phasing
RESOLVE	2.09	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ADSC	QUANTUM	data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.1→42.74 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.95 / SU B: 1.358 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.225	6722	5 %	RANDOM
R_work	0.195	-	-	-
obs	0.196	133369	97.25 %	-

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 mean: 13.814 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.08 Å²	0 Å²	0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.1→42.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2515	0	10	625	3150

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	2582
X-RAY DIFFRACTION	r_angle_refined_deg	1.256	1.937	3507
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.292	5	320
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.516	24.135	133
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.198	15	448
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.815	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	381
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1994
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	1314
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	1832
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	450
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.156	0.2	24
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.156	0.2	50
X-RAY DIFFRACTION	r_mcbond_it	1.291	1.5	1605
X-RAY DIFFRACTION	r_mcangle_it	1.786	2	2531
X-RAY DIFFRACTION	r_scbond_it	2.506	3	1090
X-RAY DIFFRACTION	r_scangle_it	3.426	4.5	976
X-RAY DIFFRACTION	r_rigid_bond_restr	1.525	3	2695
X-RAY DIFFRACTION	r_sphericity_free	4.605	3	625
X-RAY DIFFRACTION	r_sphericity_bonded	3.59	3	2525

LS refinement shell

Resolution: 1.1→1.129 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	503	-
R_work	0.248	8966	-
obs	-	9469	94.18 %

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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