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- PDB-6bj5: Structure of the Clinically used Myxomaviral Serine Protease Inhi... -

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Basic information

Entry
Database: PDB / ID: 6bj5
TitleStructure of the Clinically used Myxomaviral Serine Protease Inhibitor 1 (SERP-1)
Components(Serine proteinase inhibitor ...) x 2
KeywordsIMMUNOSUPPRESSANT / Serpin / glycosylation / protease inhibitor
Function / homology
Function and homology information


: / serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / Serine proteinase inhibitor 1
Similarity search - Component
Biological speciesMyxoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMahon, B.P. / Lomelino, C.L. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109524 United States
CitationJournal: To Be Published
Title: Structure of the Clinically used Myxomaviral Serine Protease Inhibitor 1 (SERP-1)
Authors: Mahon, B.P. / Lomelino, C.L. / Ambadapadi, S. / Yaron, J. / Keinan, S. / Kurnikov, I. / Zhang, L. / Reeves, W. / Pinard, M.A. / Macaulay, C. / McFadden, G. / Tibbetts, S. / McKenna, R. / Lucas, A.
History
DepositionNov 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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

Downloads & links

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Assembly

Deposited unit
B: Serine proteinase inhibitor 1
F: Serine proteinase inhibitor 1
A: Serine proteinase inhibitor 1
G: Serine proteinase inhibitor 1
C: Serine proteinase inhibitor 1
H: Serine proteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,23410
Polymers124,8686
Non-polymers1,3664
Water1,04558
1
B: Serine proteinase inhibitor 1
F: Serine proteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0473
Polymers41,6232
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-38 kcal/mol
Surface area15430 Å2
MethodPISA
2
A: Serine proteinase inhibitor 1
G: Serine proteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8443
Polymers41,6232
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-39 kcal/mol
Surface area15470 Å2
MethodPISA
3
C: Serine proteinase inhibitor 1
H: Serine proteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3434
Polymers41,6232
Non-polymers7212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-40 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.012, 122.066, 130.095
Angle α, β, γ (deg.)90.00, 94.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Serine proteinase inhibitor ... , 2 types, 6 molecules BACFGH

#1: Protein Serine proteinase inhibitor 1 / / Serpin-1


Mass: 35602.535 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxoma virus (strain Lausanne) / Strain: Lausanne / Gene: SPI-1, SERP1, m008.1L / Production host: unidentified baculovirus / References: UniProt: P12393
#2: Protein Serine proteinase inhibitor 1 / / Serpin-1


Mass: 6020.045 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 316-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxoma virus (strain Lausanne) / Strain: Lausanne / Gene: SPI-1, SERP1, m008.1L / Production host: unidentified baculovirus / References: UniProt: P12393

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Sugars , 2 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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

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Non-polymers , 2 types, 59 molecules

#5: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H28O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M POTASSIUM CHLORIDE, 0.05 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.05 M TRIS-HCL PH 7.5, 10% W/V POLYETHYLENE GLYCOL (PEG) 4,000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 51618 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.86 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.602 / Num. unique obs: 2645 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW2

3lw2


Resolution: 2.5→19.83 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1990 4.31 %
Rwork0.207 --
obs0.209 46146 86.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7875 0 90 58 8023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018113
X-RAY DIFFRACTIONf_angle_d1.35410993
X-RAY DIFFRACTIONf_dihedral_angle_d16.4824888
X-RAY DIFFRACTIONf_chiral_restr0.081305
X-RAY DIFFRACTIONf_plane_restr0.0081381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5004-2.56280.3548720.26321636X-RAY DIFFRACTION45
2.5628-2.63190.326970.25312119X-RAY DIFFRACTION58
2.6319-2.70920.3487980.26392532X-RAY DIFFRACTION69
2.7092-2.79640.29221360.27312853X-RAY DIFFRACTION80
2.7964-2.8960.33611540.27473429X-RAY DIFFRACTION95
2.896-3.01160.33761750.26093563X-RAY DIFFRACTION99
3.0116-3.14820.33121580.25173610X-RAY DIFFRACTION99
3.1482-3.31340.29771550.2453569X-RAY DIFFRACTION99
3.3134-3.51990.30231630.22933574X-RAY DIFFRACTION99
3.5199-3.790.29951200.23542729X-RAY DIFFRACTION75
3.79-4.16820.2331610.17793605X-RAY DIFFRACTION99
4.1682-4.7640.21051630.14923614X-RAY DIFFRACTION99
4.764-5.97480.19011670.1583653X-RAY DIFFRACTION99
5.9748-19.82930.18081710.17493670X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -28.7253 Å / Origin y: 34.2466 Å / Origin z: 29.6432 Å
111213212223313233
T0.0569 Å20.0105 Å2-0.0032 Å2-0.0461 Å2-0.0056 Å2--0.0522 Å2
L0.0822 °2-0.0154 °20.0809 °2-0.0784 °2-0.0164 °2--0.1216 °2
S-0.0395 Å °0.0151 Å °-0.0038 Å °0.041 Å °0.0103 Å °-0.0187 Å °-0.055 Å °0.0142 Å °-0.0754 Å °
Refinement TLS groupSelection details: ALL

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