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- PDB-2c0g: Structure of PDI-related Chaperone, Wind mutant-Y53S -

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Basic information

Entry
Database: PDB / ID: 2c0g
TitleStructure of PDI-related Chaperone, Wind mutant-Y53S
ComponentsWINDBEUTEL PROTEIN
KeywordsCHAPERONE / WIND / WINDBEUTEL / PDI-DBETA / PDI / PROTEIN DISULFIDE ISOMERASE / PIPE / DORSAL-VENTRAL PATTERNING / WIND MUTANTS / 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: 1.75 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 / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0014
Polymers56,9432
Non-polymers582
Water3,009167
1
A: WINDBEUTEL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4942
Polymers28,4711
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: WINDBEUTEL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5072
Polymers28,4711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)108.476, 50.557, 98.900
Angle α, β, γ (deg.)90.00, 112.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein WINDBEUTEL PROTEIN / ERP29 HOMOLOG


Mass: 28471.430 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 (QIAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: O44342
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growpH: 6
Details: PROTEIN: 10.0MG/ML Y53S IN 5MM HEPES PH7.5, 25MM NACL, 0.0025%(V/V) BETA-MERCAPTOETHANOL RESERVOIR: 0.1M MES PH6.0, 50MM NACL, 18%(V/V) PEG 400 5% GLYCEROL CRYO: 0.1M MES PH6.0, 25%(V/V) PEG ...Details: PROTEIN: 10.0MG/ML Y53S IN 5MM HEPES PH7.5, 25MM NACL, 0.0025%(V/V) BETA-MERCAPTOETHANOL RESERVOIR: 0.1M MES PH6.0, 50MM NACL, 18%(V/V) PEG 400 5% GLYCEROL CRYO: 0.1M MES PH6.0, 25%(V/V) PEG 400, 10%(V/V)GLYCEROL,50MM NACL, pH 6.00

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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: 1.75→25 Å / Num. obs: 47523 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 3.86 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.32
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.96 / % possible all: 95.9

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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: 1.75→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.177 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2487 5 %RANDOM
Rwork0.219 ---
obs0.222 47523 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: 26.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.55 Å2
2---0.47 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 2 167 3468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223367
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9644551
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05424.737133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8815533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4041511
X-RAY DIFFRACTIONr_chiral_restr0.1370.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21560
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22397
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.041.52208
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75223492
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.00231177
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4644.51058
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 151
Rwork0.27 3304
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)
12.41560.31550.69873.00970.23992.4222-0.08940.06080.2426-0.0610.01850.0189-0.15710.02280.0709-0.1015-0.0111-0.0282-0.1137-0.0042-0.0424.764651.432261.0756
21.7285-0.4936-0.38962.0090.3961.96890.03250.0323-0.0928-0.049-0.0971-0.0549-0.06920.10830.0646-0.1026-0.00270.0129-0.0678-0.0113-0.075117.602435.257232.8236
31.7059-0.02790.22642.6045-0.27762.3826-0.0961-0.2337-0.06520.45810.06280.06840.1012-0.02120.0333-0.00280.01280.0151-0.09810.0008-0.086420.544231.980974.5928
44.6466-0.57291.31275.85113.83888.0434-0.02010.42380.07980.04250.2714-0.25110.55070.8452-0.25140.05390.0796-0.02250.1024-0.0502-0.081839.09542.953999.2271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1024 - 1146
2X-RAY DIFFRACTION2A1147 - 1251
3X-RAY DIFFRACTION3B1024 - 1146
4X-RAY DIFFRACTION4B1147 - 1248

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