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- PDB-3chl: Crystal Structure of Alpha-14 Giardin with magnesium bound -

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Basic information

Entry
Database: PDB / ID: 3chl
TitleCrystal Structure of Alpha-14 Giardin with magnesium bound
ComponentsAlpha-14 giardin
KeywordsMETAL BINDING PROTEIN / Magnesium-binding / Annexin
Function / homology
Function and homology information


1-phosphatidylinositol binding / cell projection organization / phosphatidylethanolamine binding / calcium-dependent phospholipid binding / motile cilium / phosphatidylserine binding / heparin binding / calcium ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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 / MAD / Resolution: 1.9 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_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)38,6612
Polymers38,6371
Non-polymers241
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.859, 133.859, 69.668
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM magnesium chloride, 100 mM sodium citrate pH 5.0, and 15% (w/v) PEG 4000 , VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979, 0.91216, 0.9793, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.912161
30.97931
40.97951
ReflectionResolution: 1.9→66.96 Å / Num. all: 36608 / Num. obs: 36608 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97926.64-8.33
13 wavelength20.97964.03-2.71
13 wavelength30.97964.06-10.51
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se21.0980.1870.3540.3330.721
2Se31.7610.0520.3870.210.823
3Se26.3690.0280.5190.1290.777
4Se27.2120.0840.4380.2030.703
5Se37.0140.4190.2680.1520.784
6Se34.9660.5040.4660.1460.745
7Se48.6090.6010.3110.0650.73
Phasing dmFOM : 0.81 / FOM acentric: 0.81 / FOM centric: 0 / Reflection: 15556 / Reflection acentric: 15556 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
7.1-44.2920.960.96677677
4.5-7.10.950.9520952095
3.6-4.50.930.9326522652
3.1-3.60.890.8926542654
2.7-3.10.740.7446824682
2.5-2.70.570.5727962796

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Processing

Software
NameVersionClassificationNB
SOLVE2.09phasing
RESOLVE2.09phasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.872 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1828 5 %RANDOM
Rwork0.199 ---
obs0.201 36571 99.65 %-
all-36571 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.236 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.34 Å20 Å2
2---0.69 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 1 169 2699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222578
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9643477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.35923.629124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3715468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1171520
X-RAY DIFFRACTIONr_chiral_restr0.1050.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021941
X-RAY DIFFRACTIONr_nbd_refined0.2120.21237
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.26
X-RAY DIFFRACTIONr_mcbond_it1.1481.51609
X-RAY DIFFRACTIONr_mcangle_it1.94922512
X-RAY DIFFRACTIONr_scbond_it2.82831101
X-RAY DIFFRACTIONr_scangle_it4.2744.5965
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 139 -
Rwork0.272 2583 -
all-2722 -
obs--99.31 %

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