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- PDB-2c0f: Structure of Wind Y53F mutant -

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Basic information

Entry
Database: PDB / ID: 2c0f
TitleStructure of Wind Y53F mutant
ComponentsWINDBEUTEL PROTEIN
KeywordsCHAPERONE / DORSAL-VENTRAL PATTERNING / PDI / PDI-DBETA / PIPE / PROTEIN DISULFIDE ISOMERASE / WIND / WINDBEUTEL / WIND MUTANT / DEVELOPMENTAL PROTEIN / ENDOPLASMIC RETICULUM
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
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsSevvana, M. / Ma, Q. / Barnewitz, K. / Guo, C. / Soling, H.-D. / Ferrari, D.M. / Sheldrick, G.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structural Elucidation of the Pdi-Related Chaperone Wind with the Help of Mutants.
Authors: Sevvana, M. / Biadene, M. / Ma, Q. / Guo, C. / Soling, H.-D. / Sheldrick, G.M. / Ferrari, D.M.
#1: Journal: 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. / Soeling, H.-D. / Uson, I. / Ferrari, D.M. / Sheldrick, G.M.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Mapping of a Sustrate Binding Site in the Protein Disulfide Isomerase-Related Chaperone Wind Based on Protein Function and Crystal Structure
Authors: Barnewitz, K. / Guo, C. / Sevvana, M. / Ma, Q. / Sheldrick, G.M. / Soeling, H.-D. / Ferrari, D.M.
History
DepositionSep 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WINDBEUTEL PROTEIN
B: WINDBEUTEL PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,0632
Polymers57,0632
Non-polymers00
Water1,76598
1
A: WINDBEUTEL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5321
Polymers28,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: WINDBEUTEL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5321
Polymers28,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.444, 51.719, 100.655
Angle α, β, γ (deg.)90.00, 112.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein WINDBEUTEL PROTEIN / ERP29 HOMOLOG


Mass: 28531.523 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: O44342
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growpH: 5.8
Details: PROTEIN: 18.0MG/ML Y53F IN 5MM HEPES PH7.5, 25MM LICL, 0.0025%(V/V) BETA-MERCAPTOETHANOL RESERVOIR: 0.1M MES PH5.8, 50MM LICL, 18%(V/V) PEG 400 CRYO: 0.1M MES PH6.0, 25%(V/V) PEG 400,50MM LICL, pH 5.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8976
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8976 Å / Relative weight: 1
ReflectionResolution: 2.28→20 Å / Num. obs: 22333 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 1.77 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.94
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.26 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OVN

1ovn


Resolution: 2.28→20.24 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.323 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1216 5.2 %THIN SHELLS
Rwork0.219 ---
obs0.222 22333 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.47 Å2
2---0.65 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.28→20.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 0 98 3353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0223317
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3771.9624494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3035449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52924.308130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56615484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6161512
X-RAY DIFFRACTIONr_chiral_restr0.1690.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022542
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21078
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22150
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2671.52351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9623470
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.37931202
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6154.51024
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.34 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 135
Rwork0.25 1357
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2895-0.15850.22062.57130.21861.39340.0014-0.03660.13050.1044-0.00210.0681-0.006-0.10860.0008-0.08160.0057-0.0027-0.05170.0195-0.0099-7.64511.223730.3672
21.04610.2958-0.01740.89180.06111.05140.06320.02240.0103-0.0088-0.04340.0568-0.0981-0.1161-0.0197-0.03640.00590.0038-0.0292-0.0049-0.0427-1.6086-4.885659.5162
30.96570.42350.0432.4451-0.24881.8815-0.1410.0648-0.1127-0.22930.1001-0.16820.157-0.08350.04090.0066-0.02270.0126-0.0820.0021-0.0506-3.6946-8.242316.7738
43.9721.13711.15681.6911-1.90274.7442-0.0828-0.28980.0229-0.16990.05370.01660.238-0.22940.0291-0.0647-0.0353-0.0178-0.03540.0166-0.0728-23.0633.1294-7.7463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 146
2X-RAY DIFFRACTION2A147 - 251
3X-RAY DIFFRACTION3B24 - 146
4X-RAY DIFFRACTION4B147 - 245

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