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- PDB-3chk: Calcium bound structure of alpha-14 giardin -

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Basic information

Entry
Database: PDB / ID: 3chk
TitleCalcium bound structure of alpha-14 giardin
ComponentsAlpha-14 giardin
KeywordsMETAL BINDING PROTEIN / Calcium-binding / Annexin
Function / homology
Function and homology information


calcium-dependent phospholipid binding / cell projection organization / motile cilium / phosphatidylserine binding / calcium ion binding / plasma membrane / cytoplasm
Similarity search - Function
Annexin E1, fourth repeat / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile.
Similarity search - Domain/homology
Alpha-14 giardin / Annexin E1
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsPathuri, P. / Luecke, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Apo and calcium-bound crystal structures of cytoskeletal protein alpha-14 giardin (annexin E1) from the intestinal protozoan parasite Giardia lamblia
Authors: Pathuri, P. / Nguyen, E.T. / Ozorowski, G. / Svard, S.G. / Luecke, H.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: Alpha-14 giardin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8386
Polymers38,6371
Non-polymers2005
Water6,612367
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.301, 50.018, 71.819
Angle α, β, γ (deg.)90.000, 110.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-14 giardin


Mass: 38637.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Gene: Alpha-14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VPP4, UniProt: Q9NFS4*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM calcium chloride, 100 mM bis-Tris pH 6.5, and 24% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 38460 / Num. obs: 38460 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.385 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1932 5 %RANDOM
Rwork0.202 ---
obs0.203 38449 97.02 %-
all-38449 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.172 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å2-0.48 Å2
2--1.3 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 5 367 2808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222483
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9623346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9525302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.59223.554121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99515452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4771520
X-RAY DIFFRACTIONr_chiral_restr0.0940.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021873
X-RAY DIFFRACTIONr_nbd_refined0.2080.21326
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2274
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.225
X-RAY DIFFRACTIONr_mcbond_it0.9311.51545
X-RAY DIFFRACTIONr_mcangle_it1.51122409
X-RAY DIFFRACTIONr_scbond_it2.55531070
X-RAY DIFFRACTIONr_scangle_it3.7384.5937
LS refinement shellResolution: 1.65→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 117 -
Rwork0.262 2230 -
all-2347 -
obs--80.9 %

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