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- PDB-3njh: D37A mutant of SO1698 protein, an aspartic peptidase from Shewane... -

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Basic information

Entry
Database: PDB / ID: 3njh
TitleD37A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis.
ComponentsPeptidase
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: 1.94 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 14, 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
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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
C: Peptidase
D: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,02911
Polymers54,7304
Non-polymers2987
Water5,711317
1
A: Peptidase
B: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4685
Polymers27,3652
Non-polymers1033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-49 kcal/mol
Surface area11990 Å2
MethodPISA
2
C: Peptidase
D: Peptidase
hetero molecules

C: Peptidase
D: Peptidase
hetero molecules

C: Peptidase
D: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,68118
Polymers82,0956
Non-polymers58612
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 area15570 Å2
ΔGint-201 kcal/mol
Surface area28830 Å2
MethodPISA
3
C: Peptidase
D: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5606
Polymers27,3652
Non-polymers1954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-48 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.986, 97.986, 65.844
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
Peptidase


Mass: 13682.532 Da / Num. of mol.: 4 / Mutation: D37A
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M calcium chloride, 0.1 M Bis-Tris buffer, 45% 2-methyl-2,4-pentanediol, pH 6.5, 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: Apr 23, 2006
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.354
11h+k,-k,-l20.188
11-h,-k,l30.163
11h,-h-k,-l40.295
ReflectionResolution: 1.94→39.3 Å / Num. all: 51991 / Num. obs: 51991 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.132 / Χ2: 2.323 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.94-1.975.10.7182.1226300.902100
1.97-2.015.30.6525550.956100
2.01-2.055.40.53626201.1100
2.05-2.095.50.47526001.212100
2.09-2.145.50.41326451.5100
2.14-2.185.50.37826131.662100
2.18-2.245.60.36125571.698100
2.24-2.35.50.31526001.923100
2.3-2.375.50.28825812.205100
2.37-2.445.50.26626392.336100
2.44-2.535.50.24225302.546100
2.53-2.635.50.21226452.906100
2.63-2.755.50.20226002.871100
2.75-2.95.40.17925813.31100
2.9-3.085.40.15626063.371100
3.08-3.325.40.13325873.44100
3.32-3.655.40.1226333.413100
3.65-4.185.40.10725703.357100
4.18-5.265.50.09326033.01100
5.26-505.70.07125962.67199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
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: 1.94→39.3 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.936 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.019 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1524 5184 10 %RANDOM
Rwork0.127 ---
all0.1296 51985 --
obs0.1296 51985 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.75 Å2 / Biso mean: 23.0839 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-5.26 Å20 Å20 Å2
2--5.26 Å20 Å2
3----10.53 Å2
Refinement stepCycle: LAST / Resolution: 1.94→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 12 317 3973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223788
X-RAY DIFFRACTIONr_bond_other_d0.0010.022400
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9715197
X-RAY DIFFRACTIONr_angle_other_deg1.09636000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.00327.143154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73215620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.741154
X-RAY DIFFRACTIONr_chiral_restr0.1270.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
X-RAY DIFFRACTIONr_mcbond_it0.7821.52440
X-RAY DIFFRACTIONr_mcbond_other0.2291.51005
X-RAY DIFFRACTIONr_mcangle_it1.25624014
X-RAY DIFFRACTIONr_scbond_it1.97131348
X-RAY DIFFRACTIONr_scangle_it2.8954.51170
LS refinement shellResolution: 1.944→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 408 -
Rwork0.156 3437 -
all-3845 -
obs-3845 98.89 %
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)
11.25720.5628-0.130.86490.31720.79740.1715-0.07490.3298-0.0181-0.08930.2062-0.20570.0304-0.08220.07820.01640.06390.0842-0.00340.175138.684-8.848519.2331
20.77860.4568-0.15710.815-0.00021.11030.0453-0.00640.0507-0.1136-0.01680.24820.109-0.1608-0.02860.07050.0229-0.01660.11150.02980.171326.7239-27.043412.4822
30.67120.0691-0.00541.82750.33511.35840.04940.01930.0679-0.04050.0171-0.312-0.09430.2133-0.06660.0305-0.00690.04510.1007-0.00830.164721.79190.6846-20.3016
41.18740.28570.2221.33730.11281.3348-0.01490.009-0.19540.08390.0396-0.09220.2325-0.0068-0.02470.06980.0322-0.01020.04710.01090.130611.9921-18.8664-13.5882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 124
2X-RAY DIFFRACTION1A501 - 507
3X-RAY DIFFRACTION2B4 - 124
4X-RAY DIFFRACTION2B502
5X-RAY DIFFRACTION3C4 - 123
6X-RAY DIFFRACTION3C503 - 506
7X-RAY DIFFRACTION4D4 - 125
8X-RAY DIFFRACTION4D504 - 505

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