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- PDB-2qaa: Crystal structure of the second tetrahedral intermediates of SGPB... -

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Basic information

Entry
Database: PDB / ID: 2qaa
TitleCrystal structure of the second tetrahedral intermediates of SGPB at pH 7.3
ComponentsStreptogrisin-B
KeywordsHYDROLASE / CHYMOTRYPSIN-TYPE SERINE PEPTIDASE / SECOND TETRAHEDRAL INTERMEDIATES / SINGLE AMINO ACIDS / BETA BARRELS / ALPHA HELIX
Function / homology
Function and homology information


streptogrisin B / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / LEUCINE / TYROSINE / Streptogrisin-B
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.23 Å
AuthorsLee, T.W. / James, M.N.G.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: 1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB).
Authors: Lee, T.W. / James, M.N.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 20, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Streptogrisin-B
B: Streptogrisin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,80133
Polymers37,3062
Non-polymers2,49531
Water9,386521
1
A: Streptogrisin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,93616
Polymers18,6531
Non-polymers1,28315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Streptogrisin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,86517
Polymers18,6531
Non-polymers1,21216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Streptogrisin-B
B: Streptogrisin-B
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)477,614396
Polymers447,67824
Non-polymers29,936372
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area82080 Å2
ΔGint-1883 kcal/mol
Surface area142650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.286, 142.286, 142.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1226-

HOH

DetailsEach asymmetric unit contains two SGPB molecules. SGPB functions as a monomer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Streptogrisin-B / Serine protease B / SGPB / Pronase enzyme B


Mass: 18653.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces griseus (bacteria) / References: UniProt: P00777, streptogrisin B

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Non-polymers , 9 types, 552 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#5: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 10 mg/mL SGPB in 10 mM MgCl2 1.0 M Li2SO4, 0.1 M HEPES-NaOH pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.23→40 Å / Num. obs: 136369 / % possible obs: 99 % / Redundancy: 8.5 % / Rsym value: 0.048 / Net I/σ(I): 37.3
Reflection shellResolution: 1.23→1.27 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.404 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 1.23→40 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12713 6842 5 %RANDOM
Rwork0.11252 ---
obs0.11326 129481 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.09 Å2
Refinement stepCycle: LAST / Resolution: 1.23→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 146 521 3285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0212860
X-RAY DIFFRACTIONr_bond_other_d00.021825
X-RAY DIFFRACTIONr_angle_refined_deg2.4141.9523888
X-RAY DIFFRACTIONr_angle_other_deg4.6893.0044442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.295368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.14723.019106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.68515382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7671517
X-RAY DIFFRACTIONr_chiral_restr0.160.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023193
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02592
X-RAY DIFFRACTIONr_nbd_refined0.3720.2501
X-RAY DIFFRACTIONr_nbd_other0.2580.21982
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21403
X-RAY DIFFRACTIONr_nbtor_other0.1180.21386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2366
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5671.51841
X-RAY DIFFRACTIONr_mcbond_other2.361.5794
X-RAY DIFFRACTIONr_mcangle_it3.23122960
X-RAY DIFFRACTIONr_scbond_it4.60431019
X-RAY DIFFRACTIONr_scangle_it5.5814.5928
X-RAY DIFFRACTIONr_rigid_bond_restr2.86634685
X-RAY DIFFRACTIONr_sphericity_free19.1123564
X-RAY DIFFRACTIONr_sphericity_bonded4.43234650
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 459 -
Rwork0.253 8619 -
obs--89.76 %

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