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- PDB-3njf: Y26F mutant of SO1698 protein, an aspartic peptidase from Shewane... -

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Basic information

Entry
Database: PDB / ID: 3njf
TitleY26F mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis
Components(Peptidase) x 2
KeywordsHYDROLASE / STRUCTURAL GENOMICS / ASPARTIC PEPTIDASE / AUTOCATALYSIS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homologyDP-EP family / DP-EP family / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta / metal ion binding / Autocatalytic aspartic peptidase
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 Å
AuthorsOsipiuk, J. / Mulligan, R. / Bargassa, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase.
Authors: Osipiuk, J. / Mulligan, R. / Bargassa, M. / Hamilton, J.E. / Cunningham, M.A. / Joachimiak, A.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Oct 31, 2012Group: Derived calculations
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase


Theoretical massNumber of molelcules
Total (without water)27,4574
Polymers27,4574
Non-polymers00
Water1,26170
1
A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase

A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase

A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase


Theoretical massNumber of molelcules
Total (without water)82,37112
Polymers82,37112
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20790 Å2
ΔGint-129 kcal/mol
Surface area28200 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-22 kcal/mol
Surface area12140 Å2
MethodPISA
3
A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)13,7292
Polymers13,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-5 kcal/mol
Surface area6800 Å2
MethodPISA
4
A: Peptidase
C: Peptidase

A: Peptidase
C: Peptidase

A: Peptidase
C: Peptidase


Theoretical massNumber of molelcules
Total (without water)75,8906
Polymers75,8906
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12610 Å2
ΔGint-97 kcal/mol
Surface area29370 Å2
MethodPISA
5
C: Peptidase
D: Peptidase


Theoretical massNumber of molelcules
Total (without water)13,7292
Polymers13,7292
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-5 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.166, 100.166, 100.824
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Peptidase


Mass: 12648.341 Da / Num. of mol.: 2 / Fragment: N-terminal domain 1-116 / Mutation: Y26F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EGA7
#2: Protein/peptide Peptidase


Mass: 1080.217 Da / Num. of mol.: 2 / Fragment: C-terminal domain 117-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EGA7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CHAIN-B PEPTIDE IS A PRODUCT OF AUTOCATALYTIC CLEAVAGE DURING CRYSTALLIZATION

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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: 3.55 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 10% PEG-3000, 0.1 M sodium/potassium phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jan 31, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.47→31.2 Å / Num. all: 13378 / Num. obs: 13378 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 72.2 Å2 / Rmerge(I) obs: 0.108 / Χ2: 1.998 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.47-2.514.50.6762.116601.071100
2.51-2.564.70.6746791.188100
2.56-2.614.90.8346881.368100
2.61-2.6650.5516591.258100
2.66-2.725.10.6276761.569100
2.72-2.785.20.4876941.497100
2.78-2.855.20.4446631.708100
2.85-2.935.30.3496631.818100
2.93-3.015.20.3066842.147100
3.01-3.115.10.2626712.799100
3.11-3.2250.2126732.779100
3.22-3.354.80.26802.646100
3.35-3.54.30.1876503.20298.9
3.5-3.694.40.1056822.49699.4
3.69-3.923.80.1046422.64995
3.92-4.223.70.0836432.39895.8
4.22-4.654.10.0716672.05899.9
4.65-5.323.90.0646642.11299.4
5.32-6.73.50.0726792.20398.4
6.7-505.10.0546611.64698.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N55

3n55


Resolution: 2.47→31.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 19.52 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.36 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 642 5 %RANDOM
Rwork0.2211 ---
all0.2234 12905 --
obs0.2234 12905 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.71 Å2 / Biso mean: 52.99 Å2 / Biso min: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.47→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 0 70 1864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221860
X-RAY DIFFRACTIONr_bond_other_d0.0010.021186
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9682542
X-RAY DIFFRACTIONr_angle_other_deg0.9432962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.32327.17978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84115312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.527152
X-RAY DIFFRACTIONr_chiral_restr0.0880.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02326
X-RAY DIFFRACTIONr_mcbond_it0.7941.51194
X-RAY DIFFRACTIONr_mcbond_other0.1331.5494
X-RAY DIFFRACTIONr_mcangle_it1.46621958
X-RAY DIFFRACTIONr_scbond_it1.9343666
X-RAY DIFFRACTIONr_scangle_it3.0044.5578
LS refinement shellResolution: 2.474→2.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 62 -
Rwork0.357 913 -
all-975 -
obs-975 98.78 %
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)
11.0774-0.1857-0.1440.24970.25211.1056-0.04080.04540.1606-0.0470.0005-0.0322-0.1175-0.0280.04030.1321-0.0036-0.01040.02940.03860.12280.467221.4073-0.5434
2-5.0991.61345.606412.0296-1.3531-3.6055-0.15250.81920.65440.9717-0.1679-0.5152-0.5169-0.33850.32040.36790.0895-0.04760.02770.03330.1951-1.335832.27488.5767
30.33820.11850.11981.1268-0.07111.2942-0.026-0.06610.04910.0333-0.00170.1526-0.0876-0.10.02770.04410.03820.03080.1119-0.02270.1146-18.786510.28077.85
45.6548-2.0598-4.2524-7.28993.9399-1.43240.53330.5696-0.03810.2407-0.66850.4725-0.5403-0.27610.13520.18210.1534-0.04580.2040.01990.1686-27.234517.2426-1.1577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 116
2X-RAY DIFFRACTION2B117 - 124
3X-RAY DIFFRACTION3C3 - 116
4X-RAY DIFFRACTION4D117 - 124

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