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- PDB-2olg: Crystal structure of the serine protease domain of prophenoloxida... -

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Basic information

Entry
Database: PDB / ID: 2olg
TitleCrystal structure of the serine protease domain of prophenoloxidase activating factor-I in a zymogen form
ComponentsPro-phenoloxidase activating enzyme-I
KeywordsHYDROLASE / prophenoloxidase activating factor-I / PPAF-I / serine protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidase activity / endopeptidase activity / innate immune response / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Proteinase, regulatory CLIP domain superfamily / Regulatory CLIP domain of proteinases / Clip or disulphide knot domain / Proteinase, regulatory CLIP domain / Clip domain profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...Proteinase, regulatory CLIP domain superfamily / Regulatory CLIP domain of proteinases / Clip or disulphide knot domain / Proteinase, regulatory CLIP domain / Clip domain profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / 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
Phenoloxidase-activating factor 1
Similarity search - Component
Biological speciesHolotrichia diomphalia (beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHa, N.C. / Piao, S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the serine protease domain of prophenoloxidase activating factor-I
Authors: Piao, S. / Kim, S. / Kim, J.H. / Park, J.W. / Lee, B.L. / Ha, N.C.
History
DepositionJan 19, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pro-phenoloxidase activating enzyme-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9584
Polymers30,6001
Non-polymers3573
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.229, 53.304, 116.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pro-phenoloxidase activating enzyme-I


Mass: 30600.473 Da / Num. of mol.: 1 / Fragment: serine protease domain, residues 88-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Holotrichia diomphalia (beetle) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O97366
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.94 Å3/Da / Density % sol: 36.63 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.15M lithium sulfate, 30% polyethylene glycol 4000, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2006
RadiationMonochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 27168 / Num. obs: 26625 / % possible obs: 98.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 34
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3 / Num. unique all: 2553 / Rsym value: 0.258 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ANY

2any


Resolution: 1.7→27.42 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.671 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24454 2673 10.1 %RANDOM
Rwork0.20368 ---
all0.2078 27064 --
obs0.2078 23921 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 20 128 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222206
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9593000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63523.868106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26315350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0241519
X-RAY DIFFRACTIONr_chiral_restr0.0980.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021713
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21119
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21492
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9751.51394
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64422196
X-RAY DIFFRACTIONr_scbond_it2.2833916
X-RAY DIFFRACTIONr_scangle_it3.5364.5804
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 177 -
Rwork0.239 1705 -
obs-26625 95.73 %

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