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- PDB-1ea7: Sphericase -

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Basic information

Entry
Database: PDB / ID: 1ea7
TitleSphericase
ComponentsSERINE PROTEASE
KeywordsHYDROLASE / SERINE PROTEASE / SPHERICASE / SUBTILISIN LIKE PROTEASE
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative 36kDa protease
Similarity search - Component
Biological speciesBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.93 Å
AuthorsAlmog, O. / Gonzalez, A. / Klein, D. / Braun, S. / Shoham, G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The 0.93A Crystal Structure of Sphericase: A Calcium-Loaded Serine Protease from Bacillus Sphaericus
Authors: Almog, O. / Gonzalez, A. / Klein, D. / Greenblat, H.M. / Braun, S. / Shoham, G.
History
DepositionJul 10, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1456
Polymers31,9451
Non-polymers2005
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.280, 62.380, 46.120
Angle α, β, γ (deg.)90.00, 114.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE PROTEASE


Mass: 31944.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS SPHAERICUS (bacteria) / Strain: 2297 / References: UniProt: Q9S3L6
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 676 / 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: 1.9 Å3/Da / Density % sol: 35.24 %
Crystal growpH: 7.5 / Details: 24% PEG 6000, 5-25MM CACL2, 0.1 M HEPES, PH 7.5.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
3100 mM1dropNaCl
41 mM1dropCaCl2
55-25 mM1reservoirCaCl2
60.1 MHEPES1reservoirpH7.5
724 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 0.93→42.3 Å / Num. obs: 130213 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 8.1
Reflection shellResolution: 0.93→0.98 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 1.5 / % possible all: 53
Reflection
*PLUS
% possible obs: 97 % / Num. measured all: 934844
Reflection shell
*PLUS
% possible obs: 53 % / Rmerge(I) obs: 0.21

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD / Resolution: 0.93→42.3 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1164 7236 -20TH
all0.097 143453 --
obs0.097 -97 %-
Refinement stepCycle: LAST / Resolution: 0.93→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 5 676 2929
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.0261
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 7237 / % reflection Rfree: 5 % / Rfactor all: 0.0977 / Rfactor Rwork: 0.0969
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.261
X-RAY DIFFRACTIONs_plane_restr0.0311
X-RAY DIFFRACTIONs_chiral_restr0.107

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