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- PDB-4evf: Crystal structure of apo alpha-1 giardin -

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Basic information

Entry
Database: PDB / ID: 4evf
TitleCrystal structure of apo alpha-1 giardin
ComponentsGiardin subunit alpha-1
KeywordsMETAL BINDING PROTEIN / Annexin / Calcium-binding protein / membrane-binding protein
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 giardin / Annexin E1, fourth repeat / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Giardin subunit alpha-1
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsWeeratunga, S. / Hofmann, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Alpha-1 giardin is an annexin with highly unusual calcium-regulated mechanisms
Authors: Weeratunga, S.K. / Osman, A. / Hu, N.-J. / Wang, C.K. / Mason, L. / Svard, S. / Hope, G. / Jones, M.K. / Hofmann, A.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Giardin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)33,9421
Polymers33,9421
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.267, 58.747, 99.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Giardin subunit alpha-1 / alpha-1 giardin


Mass: 33941.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Plasmid: pRSET_6c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17063
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.2144.39THE STRUCTURAL FACTOR FILE CONTAINS FRIEDEL PAIRS.
2
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M MgCl2, 30% PEG 2000, 20mM KH2PO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX10.111.488
SYNCHROTRONAustralian Synchrotron MX221.25474, 1.25418, 1.37756
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 17, 2006
ADSC QUANTUM 315r2CCDOct 11, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.4881
21.254741
31.254181
41.377561
ReflectionResolution: 1.9→50 Å / Num. obs: 47848 / % possible obs: 0.983 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.123
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.8 % / Num. unique all: 3386 / Rsym value: 0.382 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→24.826 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.29 / σ(F): 1.39 / Phase error: 25.92 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 2252 5.11 %Random
Rwork0.1994 ---
obs0.2026 44056 96.18 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.106 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 55.04 Å2 / Biso mean: 26.3783 Å2 / Biso min: 13.13 Å2
Baniso -1Baniso -2Baniso -3
1-7.0012 Å2-0 Å20 Å2
2---7.6498 Å2-0 Å2
3---0.6485 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 286 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072417
X-RAY DIFFRACTIONf_angle_d0.9723251
X-RAY DIFFRACTIONf_dihedral_angle_d15.221913
X-RAY DIFFRACTIONf_chiral_restr0.07344
X-RAY DIFFRACTIONf_plane_restr0.004419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94130.38151490.3022496264593
1.9413-1.98640.37281210.27392537265893
1.9864-2.03610.32111540.25122559271393
2.0361-2.09110.28611290.22742518264795
2.0911-2.15260.26321360.22922592272894
2.1526-2.22210.271260.2272615274195
2.2221-2.30140.32681490.22892602275197
2.3014-2.39350.31121670.22262583275096
2.3935-2.50230.28821330.23952665279897
2.5023-2.63410.3221700.2082634280498
2.6341-2.7990.25841360.20962729286599
2.799-3.01470.26611230.19712714283799
3.0147-3.31750.26051540.189326772831100
3.3175-3.7960.22321500.17522684283499
3.796-4.7770.19091380.14652678281698
4.777-24.82820.25011170.18912521263892

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