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- PDB-1ovn: Crystal Structure and Functional Analysis of Drosophila Wind-- a ... -

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Basic information

Entry
Database: PDB / ID: 1ovn
TitleCrystal Structure and Functional Analysis of Drosophila Wind-- a PDI-Related Protein
ComponentsWindbeutel
KeywordsCHAPERONE / Wind / Windbeutel / PDI-Dbeta / PDI / protein disulfide isomerase / Pipe / dorsal-ventral patterning
Function / homology
Function and homology information


maternal specification of dorsal/ventral axis, oocyte, soma encoded / protein folding in endoplasmic reticulum / dorsal/ventral axis specification / embryo development ending in birth or egg hatching / protein secretion / regulation of multicellular organism growth / endomembrane system / endoplasmic reticulum lumen / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
Endoplasmic reticulum protein erp29 / Endoplasmic reticulum resident protein 29, C-terminal domain / Endoplasmic reticulum resident protein 29, C-terminal / ERp29, N-terminal / Endoplasmic reticulum resident protein 29 / Endoplasmic reticulum resident protein 29, C-terminal domain superfamily / Endoplasmic reticulum protein ERp29, C-terminal domain / ERp29, N-terminal domain / Endoplasmic reticulum targeting sequence. / Glutaredoxin ...Endoplasmic reticulum protein erp29 / Endoplasmic reticulum resident protein 29, C-terminal domain / Endoplasmic reticulum resident protein 29, C-terminal / ERp29, N-terminal / Endoplasmic reticulum resident protein 29 / Endoplasmic reticulum resident protein 29, C-terminal domain superfamily / Endoplasmic reticulum protein ERp29, C-terminal domain / ERp29, N-terminal domain / Endoplasmic reticulum targeting sequence. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Protein windbeutel
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsMa, Q. / Guo, C. / Barnewitz, K. / Sheldrick, G.M. / Soling, H.D. / Uson, I. / Ferrari, D.M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure and functional analysis of Drosophila Wind, a protein-disulfide isomerase-related protein.
Authors: Ma, Q. / Guo, C. / Barnewitz, K. / Sheldrick, G.M. / Soling, H.D. / Uson, I. / Ferrari, D.M.
History
DepositionMar 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / 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 / _diffrn_source.pdbx_synchrotron_site / _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: Windbeutel
B: Windbeutel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2283
Polymers57,0952
Non-polymers1331
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.678, 50.358, 98.616
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

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Components

#1: Protein Windbeutel


Mass: 28547.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Wind / Plasmid: pQE-30 (Qiagen) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: O44342
#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: mixing 6ul [5.8mg/ml Wind in 5mM HEPES pH7.5, 25mM NaCl, 0.0025%(V/V) beta-mercaptoethanol] with 3ul [0.1M MES pH6.1, 0.1M CsCl, 2mM CaCl2, 16%(V/V) PEG 300] cryo-condition: 0.1M Mes pH6.1, ...Details: mixing 6ul [5.8mg/ml Wind in 5mM HEPES pH7.5, 25mM NaCl, 0.0025%(V/V) beta-mercaptoethanol] with 3ul [0.1M MES pH6.1, 0.1M CsCl, 2mM CaCl2, 16%(V/V) PEG 300] cryo-condition: 0.1M Mes pH6.1, 20%(V/V) PEG 300, 10%(V/V)glycerol, 0.1M CsCl, 2mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.8 mg/mlprotein1drop
25 mMHEPES1droppH7.5
325 mM1dropNaCl
40.0025 %(v/v)beta-mercaptoethanol1drop
50.1 MMES1reservoirpH6.1
60.1 M1reservoirCsCl
72 mM1reservoirCaCl2
816 %(v/v)PEG3001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 31, 2002 / Details: bent mirror
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.9→37.64 Å / Num. all: 38218 / Num. obs: 38218 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 49.18 Å2 / Rsym value: 0.0565 / Net I/σ(I): 13.96
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.79 % / Mean I/σ(I) obs: 4.77 / Num. unique all: 5373 / Rsym value: 0.2759 / % possible all: 99.6
Reflection
*PLUS
% possible obs: 0.0447 %
Reflection shell
*PLUS
Lowest resolution: 2 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.1959

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MAR345data collection
SCALEPACKdata scaling
XPREPdata reduction
CCP4data scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.9→35.17 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.927 / SU ML: 0.117 / Isotropic thermal model: individual isotropic B values / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: METHOD OF MINIMIZATION: SPARSE MATRIX
RfactorNum. reflection% reflectionSelection details
Rfree0.25571 1859 4.9 %5%,THIN SHELLS
Rwork0.21584 ---
all0.2179 38216 --
obs0.2179 38216 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.42 Å2
2---0.56 Å20 Å2
3----0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.152 Å0.163 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 1 152 3448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213363
X-RAY DIFFRACTIONr_angle_refined_deg2.1321.9554563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195453
X-RAY DIFFRACTIONr_chiral_restr0.1560.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022578
X-RAY DIFFRACTIONr_nbd_refined0.2370.21691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.212
X-RAY DIFFRACTIONr_mcbond_it2.9212.52238
X-RAY DIFFRACTIONr_mcangle_it4.57953517
X-RAY DIFFRACTIONr_scbond_it5.915.51125
X-RAY DIFFRACTIONr_scangle_it8.30481046
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.338 97
Rwork0.246 2677
obs-2774
Refinement
*PLUS
Lowest resolution: 37.64 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2557 / Rfactor Rwork: 0.2158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.023
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.13

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