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- PDB-2iic: Calcium bound structure of alpha-11 giardin -

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Basic information

Entry
Database: PDB / ID: 2iic
TitleCalcium bound structure of alpha-11 giardin
ComponentsAlpha-11 giardin
KeywordsMETAL BINDING PROTEIN / calcium-protein complex / helix-turn-helix
Function / homology
Function and homology information


calcium-dependent phospholipid binding / phosphatidylserine binding / cytoskeleton organization / microtubule / calcium ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / Alpha-11 giardin annexin domain / Alpha giardin / Annexin / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsPathuri, P. / Nguyen, E.T. / Luecke, H.
CitationJournal: 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
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-11 giardin
B: Alpha-11 giardin
C: Alpha-11 giardin
D: Alpha-11 giardin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,1728
Polymers141,0124
Non-polymers1604
Water2,000111
1
A: Alpha-11 giardin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2932
Polymers35,2531
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-11 giardin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2932
Polymers35,2531
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-11 giardin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2932
Polymers35,2531
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-11 giardin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2932
Polymers35,2531
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.300, 45.285, 131.901
Angle α, β, γ (deg.)90.000, 116.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-11 giardin


Mass: 35252.930 Da / Num. of mol.: 4
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Bis-Tris pH 6.5, 24% PEG 550 MME, 50mM calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 6.8 / Number: 112381 / Rmerge(I) obs: 0.104 / Χ2: 1.12 / D res high: 2.91 Å / D res low: 50 Å / Num. obs: 30731 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.275099.410.0371.0363.6
4.976.2799.310.0681.0373.6
4.354.9799.510.071.2773.6
3.954.3599.510.0861.3743.7
3.673.9599.810.1121.2623.7
3.453.6799.610.1541.1273.7
3.283.4599.710.2031.0723.7
3.133.2899.910.2930.9963.7
3.013.1399.810.4130.9893.7
2.913.0199.410.4930.993.6
ReflectionResolution: 2.91→50 Å / Num. obs: 30731 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.104 / Χ2: 1.117 / Net I/σ(I): 6.8
Reflection shellResolution: 2.91→3.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.493 / Num. unique all: 3054 / Χ2: 0.99 / % possible all: 99.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å41.97 Å
Translation4 Å41.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→40 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.306 3012 10 %
Rwork0.264 --
obs-30080 99.6 %
Solvent computationBsol: 29.473 Å2
Displacement parametersBiso mean: 49.595 Å2
Refinement stepCycle: LAST / Resolution: 2.93→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9700 0 4 111 9815
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.491
X-RAY DIFFRACTIONc_mcbond_it1.0251.5
X-RAY DIFFRACTIONc_scbond_it1.4062
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scangle_it2.2442.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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