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- PDB-1dk5: CRYSTAL STRUCTURE OF ANNEXIN 24(CA32) FROM CAPSICUM ANNUUM -

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Basic information

Entry
Database: PDB / ID: 1dk5
TitleCRYSTAL STRUCTURE OF ANNEXIN 24(CA32) FROM CAPSICUM ANNUUM
ComponentsANNEXIN 24(CA32)
KeywordsMETAL BINDING PROTEIN / PLANT ANNEXIN / CAPSICUM ANNUUM / BELL PEPPER / CALCIUM BINDING PROTEIN
Function / homology
Function and homology information


response to water deprivation / calcium-dependent phospholipid binding / phosphatidylserine binding / response to salt stress / response to cold / response to heat / calcium ion binding / plasma membrane / cytoplasm
Similarity search - Function
Annexin D, plant / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin D, plant / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCapsicum annuum (sweet pepper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHofmann, A. / Proust, J. / Dorowski, A. / Schantz, R. / Huber, R.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Annexin 24 from Capsicum annuum. X-ray structure and biochemical characterization.
Authors: Hofmann, A. / Proust, J. / Dorowski, A. / Schantz, R. / Huber, R.
#1: Journal: FEBS Lett. / Year: 1996
Title: Characterization and Gene Expression of an Annexin During Fruit Development in Capsicum annuum
Authors: Proust, J. / Houlne, G. / Schantz, M.L. / Schantz, R.
History
DepositionDec 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANNEXIN 24(CA32)
B: ANNEXIN 24(CA32)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,05235
Polymers73,8822
Non-polymers3,17033
Water5,909328
1
A: ANNEXIN 24(CA32)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,28615
Polymers36,9411
Non-polymers1,34514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANNEXIN 24(CA32)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,76620
Polymers36,9411
Non-polymers1,82519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: ANNEXIN 24(CA32)
hetero molecules

A: ANNEXIN 24(CA32)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,05235
Polymers73,8822
Non-polymers3,17033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+1/31
Buried area9710 Å2
ΔGint-483 kcal/mol
Surface area28030 Å2
MethodPISA
4
B: ANNEXIN 24(CA32)
hetero molecules

A: ANNEXIN 24(CA32)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,05235
Polymers73,8822
Non-polymers3,17033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_764-y+2,x-y+1,z-1/31
Buried area8380 Å2
ΔGint-443 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.760, 96.760, 173.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ANNEXIN 24(CA32)


Mass: 36940.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL FUSION MAHHHHHH / Source: (gene. exp.) Capsicum annuum (sweet pepper) / Production host: Escherichia coli (E. coli) / References: UniProt: Q42657
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 3 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.7 M (NH4)2SO4, 2 mM CaCl2, 0.1 M NaAc , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 15K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.7 Mammonium sulfate11
20.1 Msodium acetate11
32 mM11CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 176558 / Num. obs: 23400 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 74.107 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.5
Reflection shellResolution: 2.8→2.96 Å / Redundancy: 4 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.5 / % possible all: 91.8
Reflection shell
*PLUS
% possible obs: 91.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Data cutoff high absF: 10000 / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
Details: NCS-AVERAGING USED, BULK SOLVENT CORRECTION USED, STRUCTURE FACTORS SCALED ANISOTROPICALLY, NCS-RESTRAINTS USED FOR 20 GROUPS
RfactorNum. reflection% reflectionSelection details
Rfree0.316 2244 10 %RANDOM
Rwork0.216 ---
obs0.216 22758 95.7 %-
Solvent computationBsol: 34.4 Å2 / ksol: 0.293 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1--9.494 Å2-7.373 Å20 Å2
2---9.494 Å20 Å2
3---18.988 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 165 328 5572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.97
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
Refine LS restraints NCSRms dev Biso : 2 Å2 / Rms dev position: 5 Å
LS refinement shellResolution: 2.8→2.82 Å / Total num. of bins used: 44 /
RfactorNum. reflection
Rfree0.385 32
Rwork0.38 353
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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