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- PDB-3brx: Crystal Structure of calcium-bound cotton annexin Gh1 -

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Basic information

Entry
Database: PDB / ID: 3brx
TitleCrystal Structure of calcium-bound cotton annexin Gh1
ComponentsAnnexin
KeywordsMEMBRANE PROTEIN / calcium binding / membrane binding / Annexin
Function / homology
Function and homology information


regulation of cellulose biosynthetic process / fruit ripening / protein trimerization / exocytic vesicle / secretion by cell / response to water deprivation / calcium-ion regulated exocytosis / calcium-dependent phospholipid binding / phosphatidylserine binding / response to salt stress ...regulation of cellulose biosynthetic process / fruit ripening / protein trimerization / exocytic vesicle / secretion by cell / response to water deprivation / calcium-ion regulated exocytosis / calcium-dependent phospholipid binding / phosphatidylserine binding / response to salt stress / response to cold / response to heat / response to oxidative stress / calcium ion binding / membrane / 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
PHOSPHATE ION / Annexin Gh1
Similarity search - Component
Biological speciesGossypium hirsutum (cotton)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHu, N.-J. / Hofmann, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The crystal structure of calcium-bound annexin Gh1 from Gossypium hirsutum and its implications for membrane binding mechanisms of plant annexins.
Authors: Hu, N.-J. / Yusof, A.M. / Winter, A. / Osman, A. / Reeve, A.K. / Hofmann, A.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7509
Polymers36,1551
Non-polymers5958
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Annexin
hetero molecules

A: Annexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,50018
Polymers72,3102
Non-polymers1,19016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area4550 Å2
ΔGint-121 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.663, 132.663, 61.338
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Annexin / Annexin Gh1


Mass: 36154.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gossypium hirsutum (cotton) / Gene: AnnGh1 / Plasmid: pRSET_6d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P93157
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 261 / 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: 4.31 Å3/Da / Density % sol: 71.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: KH2PO4/Na2HPO4, CaCl2, pH 6.0, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorDetector: CCD / Date: Dec 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→114.89 Å / Num. obs: 21804 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 5.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.645.50.3971.81729131420.397100
2.64-2.85.50.3012.51663230060.301100
2.8-2.995.60.2253.31549827790.225100
2.99-3.235.60.14751477426330.147100
3.23-3.545.60.1096.71339223990.109100
3.54-3.955.60.0847.81225221950.084100
3.95-4.565.60.0728.51084319430.072100
4.56-5.595.60.05710.5920816590.057100
5.59-7.915.40.04414.4704312930.044100
7.91-66.3750.02816.937957550.02899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.59 Å54.11 Å
Translation2.59 Å54.11 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.44 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.872 / SU B: 7.116 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1116 5.1 %RANDOM
Rwork0.193 ---
obs0.196 21788 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.322 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 28 261 2832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212605
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9723529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9715316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64823.937127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14515473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4141522
X-RAY DIFFRACTIONr_chiral_restr0.2310.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021935
X-RAY DIFFRACTIONr_nbd_refined0.2310.21411
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2228
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.217
X-RAY DIFFRACTIONr_mcbond_it0.7371.51614
X-RAY DIFFRACTIONr_mcangle_it1.33722545
X-RAY DIFFRACTIONr_scbond_it1.80431094
X-RAY DIFFRACTIONr_scangle_it2.8164.5984
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 85 -
Rwork0.267 1522 -
all-1607 -
obs--100 %

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