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- PDB-4od7: Complex structure of Proteus mirablis DsbA (C30S) with a non-cova... -

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Basic information

Entry
Database: PDB / ID: 4od7
TitleComplex structure of Proteus mirablis DsbA (C30S) with a non-covalently bound peptide PWATCDS
Components
  • (ACE)PWATCDS(NH2) Peptide
  • Thiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE/PEPTIDE / Oxidative folding protein / virulence factor maturation protein / disulfide oxidoreductase / Thioredoxin / DsbA / Dithiol exchange / DsbB / Periplasmic / OXIDOREDUCTASE-PEPTIDE complex
Function / homology
Function and homology information


disulfide oxidoreductase activity / periplasmic space
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
THIOCYANATE ION / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 Å
AuthorsKurth, F. / Premkumar, L. / Martin, J.L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of the Dithiol Oxidase DsbA Enzyme from Proteus Mirabilis Bound Non-covalently to an Active Site Peptide Ligand.
Authors: Kurth, F. / Duprez, W. / Premkumar, L. / Schembri, M.A. / Fairlie, D.P. / Martin, J.L.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein
B: Thiol:disulfide interchange protein
C: Thiol:disulfide interchange protein
D: (ACE)PWATCDS(NH2) Peptide
E: (ACE)PWATCDS(NH2) Peptide
F: (ACE)PWATCDS(NH2) Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,67610
Polymers65,4446
Non-polymers2324
Water9,764542
1
A: Thiol:disulfide interchange protein
D: (ACE)PWATCDS(NH2) Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9314
Polymers21,8152
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-16 kcal/mol
Surface area9530 Å2
MethodPISA
2
B: Thiol:disulfide interchange protein
F: (ACE)PWATCDS(NH2) Peptide


Theoretical massNumber of molelcules
Total (without water)21,8152
Polymers21,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area9570 Å2
MethodPISA
3
C: Thiol:disulfide interchange protein
E: (ACE)PWATCDS(NH2) Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9314
Polymers21,8152
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-16 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.056, 74.056, 93.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Thiol:disulfide interchange protein


Mass: 21011.627 Da / Num. of mol.: 3 / Mutation: C30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: dsbA, PMI2828 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: B4EZ68
#2: Protein/peptide (ACE)PWATCDS(NH2) Peptide


Mass: 802.875 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3350, 0.2 M KSCN, 0.2 M NDSB-221, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2012
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.597→64.13 Å / Num. all: 74969 / Num. obs: 74969 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.3
Reflection shellResolution: 1.597→1.68 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10489 / % possible all: 93.9

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OCE

4oce


Resolution: 1.597→37.718 Å / σ(F): 1.96 / Phase error: 22.46 / Stereochemistry target values: TWIN_LSQ_F
Details: the following twin law was applied in the refinement: h,-h-k,-l
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 3774 5.03 %RANDOM
Rwork0.1725 ---
all0.178 74969 --
obs0.178 74969 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.597→37.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 0 12 542 5066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174620
X-RAY DIFFRACTIONf_angle_d1.5556256
X-RAY DIFFRACTIONf_dihedral_angle_d14.4821666
X-RAY DIFFRACTIONf_chiral_restr0.071696
X-RAY DIFFRACTIONf_plane_restr0.009814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5982-1.62570.29281820.30373221X-RAY DIFFRACTION85
1.6257-1.65530.28551910.27773594X-RAY DIFFRACTION93
1.6553-1.68710.29411700.26973563X-RAY DIFFRACTION94
1.6871-1.72150.28471940.27723547X-RAY DIFFRACTION94
1.7215-1.7590.30561960.25573545X-RAY DIFFRACTION94
1.759-1.79990.28541540.25923577X-RAY DIFFRACTION95
1.7999-1.84490.25731920.23763560X-RAY DIFFRACTION94
1.8449-1.89470.24891690.22783599X-RAY DIFFRACTION95
1.8947-1.95040.23371920.22213581X-RAY DIFFRACTION94
1.9504-2.01340.23881870.22043516X-RAY DIFFRACTION94
2.0134-2.08530.232050.21273608X-RAY DIFFRACTION94
2.0853-2.16870.25111760.20293590X-RAY DIFFRACTION95
2.1687-2.26740.22332060.20023535X-RAY DIFFRACTION94
2.2674-2.38680.22642060.19293611X-RAY DIFFRACTION94
2.3868-2.53620.2021820.18773554X-RAY DIFFRACTION95
2.5362-2.73170.20731880.17673621X-RAY DIFFRACTION95
2.7317-3.00610.20291890.16673586X-RAY DIFFRACTION95
3.0061-3.43990.19481940.15063583X-RAY DIFFRACTION95
3.4399-4.32950.14861990.12183580X-RAY DIFFRACTION95
4.3295-23.46360.15081930.12193592X-RAY DIFFRACTION95
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)
10.8290.1255-0.04351.5344-1.17973.7327-0.0194-0.03950.10290.0529-0.02980.0267-0.5942-0.18750.05140.21850.0657-0.01450.1119-0.02340.1147-34.784124.821722.4453
22.18381.0592-0.82891.3407-0.64690.9605-0.07160.1533-0.0044-0.12130.10930.08890.0639-0.0386-0.04310.1584-0.0041-0.01140.1319-0.01790.13850.30637.95633.5805
31.02430.34831.10571.13030.4373.7485-0.02250.15010.0203-0.0412-0.0163-0.1055-0.10950.58840.03690.07930.00350.01820.24470.01050.11851.93063.644513.9395
49.27416.4686-0.89677.6135-1.85524.1555-0.0249-0.37120.40050.2399-0.00250.4446-0.5237-0.14670.03460.22710.0677-0.02910.1055-0.00780.1354-37.198929.79279.0588
54.95721.78581.70653.42312.7813.51140.18050.0378-0.02410.0862-0.0778-0.31640.10110.5931-0.0580.14210.00490.01890.30610.04380.11177.31394.002127.3955
61.12462.1325-0.75032.0035-2.52821.8731-0.10490.097-0.0262-0.60520.2711-0.22420.06440.0117-0.14480.190.010.02150.2225-0.04220.1725-5.290735.663417.0281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'

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