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- PDB-1n00: Annexin Gh1 from cotton -

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Basic information

Entry
Database: PDB / ID: 1n00
TitleAnnexin Gh1 from cotton
Componentsannexin Gh1
KeywordsMEMBRANE PROTEIN / annexin / membrane-binding / calcium-binding
Function / homology
Function and homology information


regulation of cellulose biosynthetic process / fruit ripening / protein trimerization / exocytic vesicle / secretion by cell / calcium-ion regulated exocytosis / calcium-dependent phospholipid binding / phosphatidylserine binding / response to oxidative stress / calcium ion binding ...regulation of cellulose biosynthetic process / fruit ripening / protein trimerization / exocytic vesicle / secretion by cell / calcium-ion regulated exocytosis / calcium-dependent phospholipid binding / phosphatidylserine binding / response to oxidative stress / calcium ion binding / 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 speciesGossypium hirsutum (cotton)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHofmann, A. / Delmer, D.P. / Wlodawer, A.
CitationJournal: Eur.J.Biochem. / Year: 2003
Title: The crystal structure of annexin Gh1 from Gossypium hirsutum reveals an unusual S3 cluster.
Authors: Hofmann, A. / Delmer, D.P. / Wlodawer, A.
History
DepositionOct 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: 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 Gh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9224
Polymers36,6341
Non-polymers2883
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.049, 61.049, 215.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

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Components

#1: Protein annexin Gh1


Mass: 36633.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gossypium hirsutum (cotton) / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P93157
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
Temperature: 285 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10-1 M1dropNaCl
220 %saturatedHEPES1droppH8.0
3230-350 mM1dropNaCl
41.7 Mammonium sulfate1reservoir
50.1 MHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 27412 / Num. obs: 27412 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7 % / Biso Wilson estimate: 30.2 Å2
Reflection shellResolution: 2.1→2.23 Å / % possible all: 93.6
Reflection
*PLUS
Num. measured all: 808320 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.433

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→37.72 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2656 9.9 %RANDOM
Rwork0.219 ---
obs0.219 26710 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.8904 Å2 / ksol: 0.371176 e/Å3
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.02 Å26.06 Å20 Å2
2--4.02 Å20 Å2
3----8.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 15 181 2745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.713
X-RAY DIFFRACTIONc_mcangle_it3.823.5
X-RAY DIFFRACTIONc_scbond_it3.473.5
X-RAY DIFFRACTIONc_scangle_it4.54
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 419 10.1 %
Rwork0.3 3750 -
obs--93.6 %
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
Refinement
*PLUS
Num. reflection obs: 24054 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
LS refinement shell
*PLUS
Rfactor Rwork: 0.3

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