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- PDB-1bq7: DSBA MUTANT P151A, ROLE OF THE CIS-PROLINE IN THE ACTIVE SITE OF DSBA -

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Basic information

Entry
Database: PDB / ID: 1bq7
TitleDSBA MUTANT P151A, ROLE OF THE CIS-PROLINE IN THE ACTIVE SITE OF DSBA
ComponentsPROTEIN (DISULFIDE OXIDOREDUCTASE)
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / PROTEIN DISULFIDE ISOMERASE / PROTEIN FOLDING / REDOX PROTEIN / REDOX-ACTIVE CENTER
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 ...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: 2.8 Å
AuthorsCharbonnier, J.-B. / Stura, E.A.
Citation
Journal: Protein Sci. / Year: 1999
Title: On the role of the cis-proline residue in the active site of DsbA.
Authors: Charbonnier, J.B. / Belin, P. / Moutiez, M. / Stura, E.A. / Quemeneur, E.
#1: Journal: Protein Sci. / Year: 1997
Title: Structural Analysis of Three His32 Mutants of DsbA: Support for an Electrostatic Role of His32 in DsbA Stability
Authors: Guddat, L. / Bardwell, J.C. / Glockshuber, R. / Huber-Wunderlich, M. / Zander, T. / Martin, J.L.
#2: Journal: Structure / Year: 1995
Title: Thioredoxin-A Fold for All Reasons
Authors: Martin, J.L.
History
DepositionAug 21, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 20, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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

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Assembly

Deposited unit
A: PROTEIN (DISULFIDE OXIDOREDUCTASE)
B: PROTEIN (DISULFIDE OXIDOREDUCTASE)
C: PROTEIN (DISULFIDE OXIDOREDUCTASE)
D: PROTEIN (DISULFIDE OXIDOREDUCTASE)
E: PROTEIN (DISULFIDE OXIDOREDUCTASE)
F: PROTEIN (DISULFIDE OXIDOREDUCTASE)


Theoretical massNumber of molelcules
Total (without water)126,7746
Polymers126,7746
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.900, 190.700, 67.100
Angle α, β, γ (deg.)90.00, 111.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.619, -0.031, -0.784), (-0.158, -0.984, -0.087), (-0.769, 0.178, -0.614)44.892, 229.661, 71.455
2given(-0.547, 0.241, 0.801), (0.835, 0.096, 0.542), (0.054, 0.966, -0.254)-55.246, 86.771, -21.763
3given(0.839, 0.469, 0.276), (0.471, -0.88, 0.062), (0.271, 0.078, -0.959)-72.4, 168.215, 53.491
4given(-0.979, 0.109, 0.173), (-0.198, -0.284, -0.938), (-0.053, -0.953, 0.299)52.486, 160.42999, 103.667
5given(-0.107, -0.593, -0.798), (0.463, 0.681, -0.568), (0.88, -0.43, 0.202)-62.967, 106.601, 110.167

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Components

#1: Protein
PROTEIN (DISULFIDE OXIDOREDUCTASE) / DSBA


Mass: 21128.988 Da / Num. of mol.: 6 / Mutation: P151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): DSBA MINUS STRAIN / References: UniProt: P24991, UniProt: P0AEG4*PLUS
Compound detailsTHERE ARE SIX MOLECULES IN THE ASYMMETRIC UNIT. EACH CONTAINS 186 RESIDUES THE ACTIVE SITE ...THERE ARE SIX MOLECULES IN THE ASYMMETRIC UNIT. EACH CONTAINS 186 RESIDUES THE ACTIVE SITE DISULFIDE RESIDUES ARE CYS 30 AND CYS 33. HIS 32 SIDE CHAIN IS IN G+ AND T CONFORMATION IN DSBA WILD TYPE (PDB CODE 1FVK). IN DSBA P151A MUTANT, HIS32 IS IN G-COMFORMATION IN MOLECULES A,B,C,F AND IN G+ CONFORMATION IN MOLECULES D,E
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: 3.05 Å3/Da / Density % sol: 59.51 %
Crystal growpH: 6.5
Details: 25% PEG 8,000 100 MM NACL 100 MM SODIUM CACODYLATE, PH 6.5 10% DMSO DIFFUSION VAPOR AT ROOM TEMPERATURE, SEEDING
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-25 %(w/v)PEG80001reservoir
21 %MPD1reservoir
30.1 Mcacodylate1reservoir
40.5 %MPD1drop
510-12.5 %(w/v)PEG80001drop
60.05 Mcacodylate1drop
711 mg/mlDsbA1drop

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorDate: Jul 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 31364 / % possible obs: 84.6 % / Observed criterion σ(I): 0.3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 13.3
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.475 / % possible all: 87.7
Reflection
*PLUS
Num. measured all: 117916
Reflection shell
*PLUS
% possible obs: 87.9 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
AMoREphasing
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVK

1fvk


Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 1
Details: PRO 151 IS MUTATED TO ALANINE. PEPTIDE BOND VAL150-PRO151 IS IN CIS CONFORMATION IN WILD TYPE DSBA. IT IS IN TRANS-CONFORMATION IN MUTANT DSBA PRO 151 ALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1553 5 %RANDOM
Rwork0.218 ---
obs0.218 31338 85 %-
Displacement parametersBiso mean: 53.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8772 0 0 0 8772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev position (Å)Weight position
11X-RAY DIFFRACTION0.210.07
22X-RAY DIFFRACTION0.240.03
33X-RAY DIFFRACTION0.520.15
LS refinement shellResolution: 2.8→2.92 Å
RfactorNum. reflection% reflection
Rfree0.418 98 4.5 %
Rwork0.348 2273 -
obs--88 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / σ(F): 1 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.418 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.348

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