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- PDB-2c0e: Structure of PDI-related Chaperone, Wind with his-tag on C-terminus. -

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Basic information

Entry
Database: PDB / ID: 2c0e
TitleStructure of PDI-related Chaperone, Wind with his-tag on C-terminus.
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: 2.35 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 1, 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 / Version format compliance
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.3Dec 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 / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)57,0952
Polymers57,0952
Non-polymers00
Water1,946108
1
A: WINDBEUTEL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5481
Polymers28,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: WINDBEUTEL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5481
Polymers28,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.782, 50.368, 98.675
Angle α, β, γ (deg.)90.00, 112.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2025-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHRAA25 - 1407 - 122
21THRTHRTHRTHRBB25 - 1407 - 122
12ILEILEHISHISAA150 - 245132 - 227
22ILEILEHISHISBB150 - 245132 - 227

NCS ensembles :
ID
1
2

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Components

#1: Protein WINDBEUTEL PROTEIN / WIND MUTANT / ERP29 HOMOLOG


Mass: 28547.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WIND WITH HIS-TAG ON C-TERMINUS / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSSIBLE CHAPERONE PROTEIN INVOLVED IN DORSOVENTRAL AXIS PATTERNING IN EARLY EMBRYOS
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 %
Crystal growpH: 6.2
Details: PROTEIN: 15.0MG/ML WIND IN 5MM HEPES PH7.5, 25MM NACL, 0.0025%(V/V) BETA-MERCAPTOETHANOL RESERVOIR: 0.1M MES PH6.1, 50MM NACL, 18%(V/V) PEG 400 CRYO: 0.1M MES PH6.1, 25%(V/V) PEG 400, ...Details: PROTEIN: 15.0MG/ML WIND IN 5MM HEPES PH7.5, 25MM NACL, 0.0025%(V/V) BETA-MERCAPTOETHANOL RESERVOIR: 0.1M MES PH6.1, 50MM NACL, 18%(V/V) PEG 400 CRYO: 0.1M MES PH6.1, 25%(V/V) PEG 400, 10%(V/V)GLYCEROL, 50MM NACL, pH 6.20

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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: 2.35→20 Å / Num. obs: 19292 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 4.11 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.05
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 9.46 / % possible all: 99.2

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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: 2.35→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.87 / SU B: 17.576 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1044 5.1 %RANDOM
Rwork0.226 ---
obs0.23 19292 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.09 Å2
2---0.94 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 0 108 3395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223354
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.964549
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9715450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31924.122131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18715491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7181512
X-RAY DIFFRACTIONr_chiral_restr0.1410.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022562
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.21486
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22285
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9561.52284
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50323498
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.89531223
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0824.51051
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1464medium positional0.30.5
2384medium positional0.440.5
1361loose positional0.575
2251loose positional0.475
1464medium thermal1.162
2384medium thermal1.222
1361loose thermal2.1410
2251loose thermal2.4610
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 77
Rwork0.236 1399
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)
14.7389-0.51440.5654.8812-0.17293.2099-0.09190.09380.2786-0.3048-0.0773-0.0495-0.14130.12420.1692-0.1591-0.0487-0.03-0.13720.0099-0.09577.992155.060661.2226
23.1502-1.3039-0.38673.25720.46932.78160.07230.0323-0.02570.0813-0.0876-0.1487-0.06740.25840.0153-0.1932-0.0255-0.0118-0.15040.0047-0.140671.577639.11232.7604
32.132-0.19850.58823.70760.85935.3274-0.2351-0.2706-0.37880.34970.06570.35970.4066-0.0890.1695-0.03510.00510.0618-0.14660.0183-0.071373.894135.631574.6988
46.8796-0.2391.81343.8622.3439.0715-0.31320.42280.23530.02760.0148-0.19440.17920.44250.2984-0.08040.017-0.0356-0.0427-0.0047-0.037993.390246.654598.9824
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 - 248

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