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- PDB-2qa9: Crystal structure of the second tetrahedral intermediates of SGPB... -

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Basic information

Entry
Database: PDB / ID: 2qa9
TitleCrystal structure of the second tetrahedral intermediates of SGPB at pH 4.2
Components
  • 4-mer peptide DAIY
  • Streptogrisin-B
KeywordsHYDROLASE / CHYMOTRYPSIN-TYPE SERINE PEPTIDASE / SECOND TETRAHEDRAL INTERMEDIATE / TETRAPEPTIDE / 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
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_special_symmetry / 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
E: Streptogrisin-B
I: 4-mer peptide DAIY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,73711
Polymers19,1342
Non-polymers6039
Water4,972276
1
E: Streptogrisin-B
I: 4-mer peptide DAIY
hetero molecules

E: Streptogrisin-B
I: 4-mer peptide DAIY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,47422
Polymers38,2674
Non-polymers1,20718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5410 Å2
ΔGint-91 kcal/mol
Surface area13960 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-26 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.461, 107.470, 36.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-421-

SO4

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Components

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Protein / Protein/peptide , 2 types, 2 molecules EI

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


Mass: 18653.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces griseus (bacteria) / References: UniProt: P00777, streptogrisin B
#2: Protein/peptide 4-mer peptide DAIY


Mass: 480.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: AUTO-PROTEOLYTIC PRODUCT / Source: (natural) Streptomyces griseus (bacteria) / References: UniProt: P00777*PLUS

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Non-polymers , 5 types, 285 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsAUTHOR'S STATEMENT: BASED ON THE ELECTRON DENSITY MAP, 1/3 OF CONFORMER A OF RESIDUE MET180 OF ...AUTHOR'S STATEMENT: BASED ON THE ELECTRON DENSITY MAP, 1/3 OF CONFORMER A OF RESIDUE MET180 OF CHAIN E MIGHT HAVE BEEN OXIDIZED TO BECOME METHIONINE SULFOXIDE (SME). THE RESIDUE TYPE OF E-180 IS SET AT MET TO REFLECT THE DOMINANT FORM OF THE RESIDUE.

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10 mg/mL SGPB in 10 mM MgCl2 0.7 M KH2PO4 pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.18→20 Å / Num. obs: 56646 / % possible obs: 98.3 % / Redundancy: 3.6 % / Rsym value: 0.071 / Net I/σ(I): 12.4
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 5212 / Rsym value: 0.291 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SGR

1sgr


Resolution: 1.18→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.239 / SU ML: 0.026 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18204 2869 5.1 %RANDOM
Rwork0.1454 ---
obs0.14727 53726 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2--0 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 34 276 1653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0211446
X-RAY DIFFRACTIONr_bond_other_d0.0130.02918
X-RAY DIFFRACTIONr_angle_refined_deg2.4671.9471966
X-RAY DIFFRACTIONr_angle_other_deg1.7653.0042240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.3685189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.16322.8353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.37415187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.659159
X-RAY DIFFRACTIONr_chiral_restr0.1580.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021624
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02303
X-RAY DIFFRACTIONr_nbd_refined0.2320.2262
X-RAY DIFFRACTIONr_nbd_other0.2210.21025
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2726
X-RAY DIFFRACTIONr_nbtor_other0.0950.2789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.248
X-RAY DIFFRACTIONr_mcbond_it2.9731.51139
X-RAY DIFFRACTIONr_mcbond_other1.5431.5403
X-RAY DIFFRACTIONr_mcangle_it3.42321507
X-RAY DIFFRACTIONr_scbond_it4.5633599
X-RAY DIFFRACTIONr_scangle_it5.2674.5457
X-RAY DIFFRACTIONr_rigid_bond_restr2.51232869
X-RAY DIFFRACTIONr_sphericity_free15.0073292
X-RAY DIFFRACTIONr_sphericity_bonded4.84632342
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 176 -
Rwork0.207 3583 -
obs--89.84 %

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