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- PDB-2q4c: Ensemble refinement of the protein crystal structure of annexin f... -

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Basic information

Entry
Database: PDB / ID: 2q4c
TitleEnsemble refinement of the protein crystal structure of annexin from Arabidopsis thaliana gene At1g35720
ComponentsAnnexin D1
KeywordsMETAL BINDING PROTEIN / Ensemble Refinement / Refinement Methodology Development / AT1G35720 / ANNEXIN / MEMBRANE-BINDING / CALCIUM-BINDING / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


phloem sucrose unloading / root hair tip / primary root development / plant-type cell wall / potassium ion export across plasma membrane / thylakoid / apoplast / response to abscisic acid / response to water deprivation / plasmodesma ...phloem sucrose unloading / root hair tip / primary root development / plant-type cell wall / potassium ion export across plasma membrane / thylakoid / apoplast / response to abscisic acid / response to water deprivation / plasmodesma / plant-type vacuole / calcium-dependent phospholipid binding / response to osmotic stress / chloroplast stroma / response to salt stress / response to cold / chloroplast / peroxidase activity / calcium ion transmembrane transport / response to heat / copper ion binding / calcium ion binding / protein homodimerization activity / mitochondrion / zinc ion binding / ATP binding / nucleus / membrane / plasma membrane / cytosol
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 speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.508 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Annexin D1
B: Annexin D1


Theoretical massNumber of molelcules
Total (without water)72,4252
Polymers72,4252
Non-polymers00
Water5,062281
1
A: Annexin D1


Theoretical massNumber of molelcules
Total (without water)36,2131
Polymers36,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Annexin D1


Theoretical massNumber of molelcules
Total (without water)36,2131
Polymers36,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.543, 96.936, 226.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Number of models8

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Components

#1: Protein Annexin D1 / AnnAt1 / Annexin A1


Mass: 36212.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Tissue: Seedling / Gene: AT1G35720, ANN1, ANNAT1, ANX23-ATH, ATOXY5, OXY5 / Plasmid: PVP-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9SYT0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.1 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1YCN.

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Data collection

DetectorType: APS-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 1YCN

1ycn


Resolution: 2.508→29.81 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 598538.688 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1ycn and the first data set in the deposited structure factor file for 1ycn ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1ycn and the first data set in the deposited structure factor file for 1ycn along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1317 4.9 %RANDOM
Rwork0.177 ---
obs0.177 27097 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.662 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1-11.75 Å20 Å20 Å2
2---3.09 Å20 Å2
3----8.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.508→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 0 281 5251
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.622
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.508-2.670.3032145.10.23139740.0214776418887.7
2.67-2.870.2712154.80.19842370.0194751445293.7
2.87-3.160.2872104.60.19143510.024778456195.5
3.16-3.620.272294.90.19344210.0184821465096.5
3.62-4.560.2212164.60.15744410.0154812465796.8
4.56-29.810.2092335.10.16243560.0145022458991.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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