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- PDB-3n55: SO1698 protein, an aspartic peptidase from Shewanella oneidensis. -

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Basic information

Entry
Database: PDB / ID: 3n55
TitleSO1698 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 / homology
Function and homology information


DP-EP family / DP-EP family / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / Autocatalytic aspartic peptidase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsOsipiuk, J. / Mulligan, R. / 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
DepositionMay 24, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJun 2, 2010ID: 2AI4
Revision 1.0Jun 2, 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
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 1.5Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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
B: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0415
Polymers13,8382
Non-polymers2033
Water2,522140
1
A: Peptidase
B: Peptidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)84,24630
Polymers83,03012
Non-polymers1,21618
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 area22930 Å2
ΔGint-375 kcal/mol
Surface area27580 Å2
MethodPISA
2
A: Peptidase
B: Peptidase
hetero molecules

A: Peptidase
B: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,08210
Polymers27,6774
Non-polymers4056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6030 Å2
ΔGint-112 kcal/mol
Surface area10810 Å2
MethodPISA
3
A: Peptidase
B: Peptidase
hetero molecules

A: Peptidase
B: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,08210
Polymers27,6774
Non-polymers4056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area4620 Å2
ΔGint-106 kcal/mol
Surface area12220 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-47 kcal/mol
Surface area6770 Å2
MethodPISA
5
A: Peptidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)77,76424
Polymers76,5496
Non-polymers1,21618
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 area15140 Å2
ΔGint-329 kcal/mol
Surface area28650 Å2
MethodPISA
6
A: Peptidase
hetero molecules

A: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9218
Polymers25,5162
Non-polymers4056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3430 Å2
ΔGint-96 kcal/mol
Surface area11170 Å2
MethodPISA
7
A: Peptidase
hetero molecules

A: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9218
Polymers25,5162
Non-polymers4056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area2030 Å2
ΔGint-90 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.997, 99.997, 100.873
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Peptidase


Mass: 12758.132 Da / Num. of mol.: 1 / Fragment: N-terminal domain 1-116
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.: 1 / 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

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Non-polymers , 4 types, 143 molecules

#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: obtained synthetically / Formula: H2O

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Details

Has protein modificationY
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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% ETHANOL, 0.1 M MES BUFFER, 0.2 M ZINC ACETATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 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: 1.57→32.9 Å / Num. obs: 27101 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.03 / Net I/σ(I): 17.8
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.66 / Num. unique all: 2466 / Χ2: 0.765 / % possible all: 84.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→32.9 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 1.757 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.168 2082 7.7 %RANDOM
Rwork0.145 ---
all0.147 27099 --
obs0.147 27099 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.52 Å2 / Biso mean: 20.372 Å2 / Biso min: 7.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.57→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 0 149 1038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022991
X-RAY DIFFRACTIONr_bond_other_d0.0030.02635
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.9791369
X-RAY DIFFRACTIONr_angle_other_deg1.02331598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.79526.97743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52115171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.485152
X-RAY DIFFRACTIONr_chiral_restr0.1210.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02175
X-RAY DIFFRACTIONr_mcbond_it1.8941.5625
X-RAY DIFFRACTIONr_mcbond_other0.6461.5255
X-RAY DIFFRACTIONr_mcangle_it2.88721036
X-RAY DIFFRACTIONr_scbond_it4.0863366
X-RAY DIFFRACTIONr_scangle_it6.1044.5320
X-RAY DIFFRACTIONr_rigid_bond_restr1.71631626
LS refinement shellResolution: 1.569→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 145 -
Rwork0.349 1716 -
all-1861 -
obs-1861 92.45 %
Refinement TLS params.Method: refined / Origin x: 1.0047 Å / Origin y: 21.124 Å / Origin z: 45.8209 Å
111213212223313233
T0.0885 Å2-0.0057 Å20.007 Å2-0.0111 Å20.0265 Å2--0.0848 Å2
L1.5451 °2-0.2172 °2-0.2523 °2-0.6398 °20.0336 °2--1.2591 °2
S0.0248 Å °0.0602 Å °0.2886 Å °-0.0455 Å °0.0175 Å °-0.0283 Å °-0.1081 Å °-0.0062 Å °-0.0423 Å °

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