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- PDB-3njl: D116A mutant of SO1698 protein, an aspartic peptidase from Shewan... -

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Basic information

Entry
Database: PDB / ID: 3njl
TitleD116A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis, at pH7.5
ComponentsPeptidaseProtease
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 / Resolution: 1.75 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 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7072
Polymers13,6831
Non-polymers241
Water2,306128
1
A: Peptidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)82,24112
Polymers82,0956
Non-polymers1466
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area13530 Å2
ΔGint-162 kcal/mol
Surface area29130 Å2
MethodPISA
2
A: Peptidase
hetero molecules

A: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4144
Polymers27,3652
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2660 Å2
ΔGint-38 kcal/mol
Surface area11560 Å2
MethodPISA
3
A: Peptidase
hetero molecules

A: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4144
Polymers27,3652
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area1760 Å2
ΔGint-33 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.151, 100.151, 100.216
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Peptidase / Protease


Mass: 13682.532 Da / Num. of mol.: 1 / Mutation: D116A
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES buffer, 0.5 M magnesium sulfate, pH 7.5, 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: Nov 13, 2005
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: 1.75→31.2 Å / Num. all: 19469 / Num. obs: 19469 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.043 / Χ2: 0.894 / Net I/σ(I): 11.1
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2.45 / Num. unique all: 1603 / Χ2: 0.961 / % possible all: 99.1

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Processing

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

3n55


Resolution: 1.75→31.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.447 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.083 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.172 988 5.1 %RANDOM
Rwork0.166 ---
all0.166 19371 --
obs0.166 19371 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.66 Å2 / Biso mean: 33.232 Å2 / Biso min: 7.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 1 128 1024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022979
X-RAY DIFFRACTIONr_bond_other_d0.0010.02623
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9721353
X-RAY DIFFRACTIONr_angle_other_deg0.90431566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.11426.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98815168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.129152
X-RAY DIFFRACTIONr_chiral_restr0.1050.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02175
X-RAY DIFFRACTIONr_mcbond_it1.0881.5625
X-RAY DIFFRACTIONr_mcbond_other0.2981.5254
X-RAY DIFFRACTIONr_mcangle_it1.85921039
X-RAY DIFFRACTIONr_scbond_it2.5073354
X-RAY DIFFRACTIONr_scangle_it4.2464.5306
LS refinement shellResolution: 1.753→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 75 -
Rwork0.379 1316 -
all-1391 -
obs-1391 97.55 %
Refinement TLS params.Method: refined / Origin x: 0.5793 Å / Origin y: 21.8105 Å / Origin z: 46.3252 Å
111213212223313233
T0.1798 Å2-0.0041 Å20.0027 Å2-0.015 Å20.03 Å2--0.1337 Å2
L1.7338 °20.1273 °2-0.353 °2-0.8153 °2-0.0237 °2--2.3808 °2
S0.0366 Å °0.0645 Å °0.3493 Å °-0.0254 Å °-0.0112 Å °0.0583 Å °-0.415 Å °-0.0313 Å °-0.0254 Å °

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