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- PDB-1un2: Crystal structure of circularly permuted CPDSBA_Q100T99: Preserve... -

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Basic information

Entry
Database: PDB / ID: 1un2
TitleCrystal structure of circularly permuted CPDSBA_Q100T99: Preserved Global Fold and Local Structural Adjustments
ComponentsTHIOL-DISULFIDE INTERCHANGE PROTEIN
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / PROTEIN DISULFIDE ISOMERASE / PROTEIN FOLDING / THIOREDOXIN / REDOX PROTEIN / DISULFIDE BOND FORMATION / CIRCULAR PERMUTATION
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space / periplasmic space / oxidoreductase activity
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbA / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsManjasetty, B.A. / Hennecke, J. / Glockshuber, R. / Heinemann, U.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of Circularly Permuted Dsba(Q100T99): Preserved Global Fold and Local Structural Adjustments
Authors: Manjasetty, B.A. / Hennecke, J. / Glockshuber, R. / Heinemann, U.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Random Circular Permutaion of Dsba Reveals Segments that are Essential for Protein Folding and Stability
Authors: Hennecke, J. / Sebbal, P. / Glockshuber, R.
History
DepositionSep 3, 2003Deposition site: PDBE / Processing site: PDBE
SupersessionSep 26, 2003ID: 1DYV
Revision 1.0Sep 26, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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
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

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Assembly

Deposited unit
A: THIOL-DISULFIDE INTERCHANGE PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,8401
Polymers21,8401
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.760, 52.590, 53.730
Angle α, β, γ (deg.)90.00, 103.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein THIOL-DISULFIDE INTERCHANGE PROTEIN / DSBA


Mass: 21839.832 Da / Num. of mol.: 1
Fragment: THIOREDOXIN-LIKE DOMAIN, HELICAL DOMAIN RESIDUES, 119-208
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BOND FORMATION PROTEIN / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PDSBA5 / Cellular location (production host): PERIPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KPNI / References: UniProt: P24991, UniProt: P0AEG4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCPDSBA_Q100T99 IS A CIRCULARLY PERMUTED VARIANT OF THE PARENT THIOL-DISULFIDE INTERCHANGE PROTEIN ...CPDSBA_Q100T99 IS A CIRCULARLY PERMUTED VARIANT OF THE PARENT THIOL-DISULFIDE INTERCHANGE PROTEIN (SEE PDB ENTRY 1A2J) SWISSPROT P24991. THE LINEAR SEQUENCE OF P24991 HAS BEEN REARRANGED TO PLACE RESIDUES 20 - 118 BEHIND RESIDUES 119 - 208 BY GENETIC ENGINEERING, N- AND C-TERMINI WERE JOINED WITH A FIVE AMINO ACID RESIDUE LINKER, GGGTG. THE NEW N-TERMINUS IS LOCATED AT RESIDUE 119 (NATIVE NUMBERING) WHILE THE NEW C-TERMINUS, NATIVE 118 HAS A THREE RESIDUE EXTENSION, LIK, WHICH IS THE RESULT OF A CLONING ARTIFACT.
Sequence detailsTHE PDB HAS CHANGED THE SEQUENCE NUMBERING IN THIS ENTRY FROM THAT USED IN THE PUBLISHED LITERATURE. ...THE PDB HAS CHANGED THE SEQUENCE NUMBERING IN THIS ENTRY FROM THAT USED IN THE PUBLISHED LITERATURE. THE AUTHORS HAVE USED THE NATIVE SEQUENCE NUMBERING WHILE THE PDB HAS RE-NUMBERED THE SEQUENCE FROM THE NEW N-TERMINUS. THIS MATCHES THE STYLE OF RESIDUE NUMBERING FOR THE CIRCULARLY PERMUTED PROTEINS IN PDB ENTRIES 1AJK AND 1AJO. THE FOLLOWING TABLE SHOWS THE CONVERSION, PDB SEQUENCE SWS P24991 AUTHOR'S SEQUENCE --------------------------------------------------------- - 1 TO 19 (SIGNAL) - 1 TO 90 119 TO 208 (DSBA) 119 TO 208 90A TO 90E - 189A TO 189E (LINKER 91 TO 189 20 TO 118 (DSBA) 20 TO 118 189A TO 189C - 99A TO 99C (C-TERM THE ALIGNMENT BETWEEN THE CIRCULARLY PERMUTED PROTEIN STUDIED HERE AND THE NATIVE DSBA PROTEIN IS GIVEN BELOW - THE LINKER BETWEEN THE NATIVE C- AND N-TERMINI IS SHOWN BETWEEN RESIDUES 90 AND 91. 10 20 30 40 50 1UN2 QTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRG P24991 QTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRG 120 130 140 150 160 60 70 80 90 91 1UN2 VPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKKGGGTGAQY P24991 VPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK-----AQY 170 180 190 200 20 100 110 120 130 140 1UN2 EDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEG P24991 EDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEG 30 40 50 60 70 150 160 170 180 189 1UN2 VKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTLIK P24991 VKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKT--- 80 90 100 110 118 THE NEW C-TERMINAL EXTENSION AROSE DURING THE CONSTRUCTION OF THE LIBRARY OF RANDOMLY CIRCULARLY PERMUTED DSBA GENES.

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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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.5
Details: 25% PEG 8000, 7-10% DMSO, 0.1M NA CACODYLATE PH 6.5
Crystal grow
*PLUS
Temperature: 291 K / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
225 %PEG80001reservoir
37-10 %DMSO1reservoir
40.1 Mcacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116
DetectorDate: Apr 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 7952 / % possible obs: 99 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 6.4 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 37723 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A2J

1a2j


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.016 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.627 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 791 10 %RANDOM
Rwork0.206 ---
obs0.211 7149 97.9 %-
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: 38.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å23.87 Å2
2---0.38 Å20 Å2
3---4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 0 82 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221479
X-RAY DIFFRACTIONr_bond_other_d0.0050.021309
X-RAY DIFFRACTIONr_angle_refined_deg1.0271.9432002
X-RAY DIFFRACTIONr_angle_other_deg0.72733057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5665184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021649
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02292
X-RAY DIFFRACTIONr_nbd_refined0.210.2349
X-RAY DIFFRACTIONr_nbd_other0.2570.21522
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.2798
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.141.5922
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33121479
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9823557
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2414.5523
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 40
Rwork0.262 412
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)
11.42221.0474-0.45212.0108-0.88292.5814-0.0172-0.037-0.140.0222-0.0336-0.02140.0560.25560.05080.0606-0.0027-0.02850.05850.04550.065120.1817-4.500224.3168
24.24880.72980.11760.4865-0.34570.6962-0.04220.5689-0.22040.02060.1013-0.17-0.0772-0.0296-0.05910.06530.00860.00130.1381-0.00290.01916.72062.41158.8382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 37
2X-RAY DIFFRACTION1A155 - 189
3X-RAY DIFFRACTION2A38 - 88
4X-RAY DIFFRACTION2A93 - 154
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.027

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