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- PDB-3njn: Q118A mutant of SO1698 protein, an aspartic peptidase from Shewan... -

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Basic information

Entry
Database: PDB / ID: 3njn
TitleQ118A 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 / Resolution: 1.25 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 1.3Oct 31, 2012Group: Derived calculations
Revision 1.4Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5737
Polymers27,3754
Non-polymers1983
Water5,278293
1
A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase
hetero molecules

A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase
hetero molecules

A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,72021
Polymers82,12512
Non-polymers5959
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area22600 Å2
ΔGint-178 kcal/mol
Surface area28430 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-45 kcal/mol
Surface area11620 Å2
MethodPISA
3
C: Peptidase
D: Peptidase
hetero molecules

A: Peptidase
B: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5737
Polymers27,3754
Non-polymers1983
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area4780 Å2
ΔGint-39 kcal/mol
Surface area12230 Å2
MethodPISA
4
A: Peptidase
B: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8464
Polymers13,6882
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-16 kcal/mol
Surface area7140 Å2
MethodPISA
5
C: Peptidase
D: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,6882
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-11 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.351, 72.351, 256.008
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-403-

CA

21A-133-

HOH

31A-269-

HOH

41C-119-

HOH

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Components

#1: Protein Peptidase


Mass: 12664.341 Da / Num. of mol.: 2 / Fragment: N-terminal domain 1-116 / Mutation: Q118A
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: 1023.167 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M calcium chloride, 0.1 M Bis-Tris buffer, 45% 2-methyl-2,4-pentanediol, pH 5.5, 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: 1.25→23.3 Å / Num. all: 64712 / Num. obs: 64712 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.045 / Χ2: 1.103 / Net I/σ(I): 14.4
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.19 / Num. unique all: 1892 / Χ2: 0.928 / % possible all: 53.7

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Processing

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

3n55


Resolution: 1.25→23.3 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.025 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.164 2580 4 %RANDOM
Rwork0.139 ---
all0.14 64392 --
obs0.14 64392 90.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.63 Å2 / Biso mean: 14.725 Å2 / Biso min: 2.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.25→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 10 293 2124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222008
X-RAY DIFFRACTIONr_bond_other_d0.0010.021300
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9782772
X-RAY DIFFRACTIONr_angle_other_deg0.95533262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2665283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.85126.62783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59115344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.896154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212239
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_mcbond_it1.8551.51269
X-RAY DIFFRACTIONr_mcbond_other0.5871.5518
X-RAY DIFFRACTIONr_mcangle_it2.83922102
X-RAY DIFFRACTIONr_scbond_it3.7283739
X-RAY DIFFRACTIONr_scangle_it5.4954.5648
X-RAY DIFFRACTIONr_rigid_bond_restr1.52433308
LS refinement shellResolution: 1.252→1.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 112 -
Rwork0.342 2745 -
all-2857 -
obs-2857 55.04 %
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)
10.3449-0.13180.00110.06780.02450.2515-0.00310.0242-0.04880.0025-0.00370.01490.0341-0.00170.00680.0705-0.0030.0020.0572-0.0070.0639-4.441120.8966102.6252
23.3722-2.50862.49732.0545-1.67531.91530.07870.018-0.2458-0.0797-0.04270.19080.1214-0.0347-0.0360.10590.00550.07510.02690.00090.168-3.16269.2042111.956
30.0852-0.0848-0.04450.2524-0.04480.43440.00170.0097-0.01020.00730.00020.0344-0.0007-0.0652-0.00190.0541-0.00320.00160.0705-0.00150.0603-20.224634.1382111.4885
44.1388-3.07794.80143.719-2.9325.72760.0337-0.2969-0.0673-0.0603-0.02550.21980.093-0.4248-0.00820.04450.0022-0.00420.1183-0.01540.0606-30.826532.3701102.8467
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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