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- PDB-3fhk: Crystal structure of APC1446, B.subtilis YphP disulfide isomerase -

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Basic information

Entry
Database: PDB / ID: 3fhk
TitleCrystal structure of APC1446, B.subtilis YphP disulfide isomerase
ComponentsUPF0403 protein yphP
Keywordsstructural genomics / unknown function / disulfide isomerase / Thioredoxin superfamily / CXC motif / Surface Entropy Reduction / SER / PSI-2 / Protein structure initiative / ISFI / Integrated Center for Structure and Function Innovation
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2150 / Bacilliredoxins BrxB/BrxA / Disulphide isomerase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0403 protein YphP
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDerewenda, U. / Boczek, T. / Cooper, D.R. / Yu, M. / Hung, L. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: Biochemistry / Year: 2009
Title: Structure and function of Bacillus subtilis YphP, a prokaryotic disulfide isomerase with a CXC catalytic motif .
Authors: Derewenda, U. / Boczek, T. / Gorres, K.L. / Yu, M. / Hung, L.W. / Cooper, D. / Joachimiak, A. / Raines, R.T. / Derewenda, Z.S.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0403 protein yphP
D: UPF0403 protein yphP
E: UPF0403 protein yphP
F: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34916
Polymers64,1974
Non-polymers1,15312
Water4,486249
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-195 kcal/mol
Surface area25890 Å2
MethodPISA
2
A: UPF0403 protein yphP
E: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6758
Polymers32,0982
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: UPF0403 protein yphP
D: UPF0403 protein yphP
F: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,01212
Polymers48,1483
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UPF0403 protein yphP
E: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6758
Polymers32,0982
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: UPF0403 protein yphP
F: UPF0403 protein yphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6758
Polymers32,0982
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.161, 68.161, 302.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsmonomer

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Components

#1: Protein
UPF0403 protein yphP


Mass: 16049.176 Da / Num. of mol.: 4 / Mutation: Q100A, E101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU21860, yphP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P54170
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M Ammonium Sulfate, 100mM Tris, 5% PEP 629., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97950, 0.9796, 0.9393
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.93931
ReflectionResolution: 2.3→30 Å / Num. all: 32111 / Num. obs: 31840 / % possible obs: 97.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 19.7
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.2 / % possible all: 82.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9 / SU ML: 0.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1593 5 %
Rwork0.1899 --
obs0.1928 31840 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.627 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 46.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.253 Å0.312 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 60 249 4793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064616
X-RAY DIFFRACTIONf_angle_d1.0176261
X-RAY DIFFRACTIONf_dihedral_angle_d18.8981692
X-RAY DIFFRACTIONf_chiral_restr0.069705
X-RAY DIFFRACTIONf_plane_restr0.004820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37420.37361260.31782461X-RAY DIFFRACTION90
2.3742-2.45910.30131230.26452533X-RAY DIFFRACTION90
2.4591-2.55760.3141370.2312596X-RAY DIFFRACTION93
2.5576-2.6740.30351390.21652663X-RAY DIFFRACTION95
2.674-2.8150.26981450.21082695X-RAY DIFFRACTION97
2.815-2.99130.28141390.20092794X-RAY DIFFRACTION98
2.9913-3.22230.26661540.19742797X-RAY DIFFRACTION100
3.2223-3.54660.25231700.172804X-RAY DIFFRACTION100
3.5466-4.05970.19081410.15352865X-RAY DIFFRACTION100
4.0597-5.11470.20571590.14562912X-RAY DIFFRACTION100
5.1147-75.54670.23341600.20163127X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.7769-0.16861.17371.63720.19212.5303-0.1055-0.2010.2357-0.0260.0101-0.0993-0.1227-0.2580.07150.01430.0113-0.01620.3013-0.06630.211170.001632.2351-28.1221
22.9858-0.25662.18673.1851-0.15864.8037-0.13460.02680.0941-0.47690.08470.2527-0.0656-0.23590.03410.28610.0167-0.05050.09570.0590.2171
32.530.4375-1.20862.3087-0.02894.3693-0.02650.03010.0074-0.0275-0.03390.12940.2572-1.16390.00760.0728-0.1019-0.04550.39980.01150.1241
42.68920.8737-0.38245.9409-1.28382.19880.08180.08620.2502-0.0304-0.2035-0.4845-0.47070.11690.03180.3857-0.01150.04410.0638-0.02180.3645
Refinement TLS groupSelection details: chain F

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