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- PDB-4ihu: Reduced form of disulfide bond oxdioreductase (DsbG) from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4ihu
TitleReduced form of disulfide bond oxdioreductase (DsbG) from Mycobacterium tuberculosis
ComponentsIsomerase DsbG
KeywordsOXIDOREDUCTASE / thioredoxin / disulfide bond isomerase / redox
Function / homology
Function and homology information


peptidoglycan-based cell wall / cell surface / plasma membrane
Similarity search - Function
Thioredoxin / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Possible conserved membrane or secreted protein / Possible conserved membrane or secreted protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsHarmston, C.A. / Goulding, C.W.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: Structural and biochemical characterization of the essential DsbA-like disulfide bond forming protein from Mycobacterium tuberculosis.
Authors: Chim, N. / Harmston, C.A. / Guzman, D.J. / Goulding, C.W.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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: Isomerase DsbG
B: Isomerase DsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2863
Polymers47,2502
Non-polymers351
Water5,386299
1
A: Isomerase DsbG
hetero molecules

A: Isomerase DsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3214
Polymers47,2502
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1280 Å2
ΔGint-25 kcal/mol
Surface area17220 Å2
MethodPISA
2
B: Isomerase DsbG

B: Isomerase DsbG


Theoretical massNumber of molelcules
Total (without water)47,2502
Polymers47,2502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area1170 Å2
ΔGint-11 kcal/mol
Surface area18040 Å2
MethodPISA
3
A: Isomerase DsbG
hetero molecules

A: Isomerase DsbG
hetero molecules

B: Isomerase DsbG

B: Isomerase DsbG


Theoretical massNumber of molelcules
Total (without water)94,5726
Polymers94,5014
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_547-x+1/2,y-1/2,-z+21
crystal symmetry operation4_557x+1/2,-y+1/2,-z+21
Buried area4350 Å2
ΔGint-42 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.030, 76.710, 86.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

21B-332-

HOH

31B-405-

HOH

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Components

#1: Protein Isomerase DsbG


Mass: 23625.238 Da / Num. of mol.: 2 / Fragment: UNP residues 46-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2969c / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6YAR2, UniProt: O33272*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 299 / 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: 49.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.9 M ammonium sulfate, 9% isopropanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97602 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2012
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97602 Å / Relative weight: 1
ReflectionResolution: 1.89→44.7 Å / Num. all: 38411 / Num. obs: 38375 / % possible obs: 99.97 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.896→1.9434 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.393 / Num. unique all: 706287 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EU3

3eu3


Resolution: 1.896→44.7 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1922 5.01 %random
Rwork0.2008 ---
obs0.2024 38370 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.896→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 1 299 3289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073078
X-RAY DIFFRACTIONf_angle_d1.1094198
X-RAY DIFFRACTIONf_dihedral_angle_d12.0661084
X-RAY DIFFRACTIONf_chiral_restr0.075490
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.896-1.94340.30991510.23942548X-RAY DIFFRACTION100
1.9434-1.9960.26881510.23442532X-RAY DIFFRACTION100
1.996-2.05470.30531160.22592585X-RAY DIFFRACTION100
2.0547-2.1210.31281250.21962583X-RAY DIFFRACTION100
2.121-2.19680.25151300.21472582X-RAY DIFFRACTION100
2.1968-2.28480.24231450.21232581X-RAY DIFFRACTION100
2.2848-2.38880.2911490.20762556X-RAY DIFFRACTION100
2.3888-2.51470.24561310.21382588X-RAY DIFFRACTION100
2.5147-2.67220.25871250.21262614X-RAY DIFFRACTION100
2.6722-2.87850.24511280.2162604X-RAY DIFFRACTION100
2.8785-3.16810.24431400.20862619X-RAY DIFFRACTION100
3.1681-3.62640.22321410.19052627X-RAY DIFFRACTION100
3.6264-4.56810.19231560.16942633X-RAY DIFFRACTION100
4.5681-44.71650.17621340.19062796X-RAY DIFFRACTION99

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