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- PDB-4r9i: Crystal structure of cysteine proteinase inhibitor Serpin18 from ... -

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Basic information

Entry
Database: PDB / ID: 4r9i
TitleCrystal structure of cysteine proteinase inhibitor Serpin18 from Bombyx mori
ComponentsSerpin-18
KeywordsHydrolase inhibitor / proteinase inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / CITRATE ANION / Serpin-18
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsGuo, P.C. / He, H.W. / Zhao, P. / Xia, Q.Y.
CitationJournal: Sci Rep / Year: 2015
Title: Structural insights into the unique inhibitory mechanism of the silkworm protease inhibitor serpin18
Authors: Guo, P.C. / Dong, Z. / Zhao, P. / Zhang, Y. / He, H.W. / Tan, X. / Zhang, W. / Xia, Q.Y.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Serpin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1954
Polymers42,9041
Non-polymers2903
Water9,332518
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.301, 109.301, 72.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serpin-18 / / serine/cysteine proteinase inhibitor


Mass: 42904.430 Da / Num. of mol.: 1 / Fragment: UNP residues 21-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Strain: DZ872 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: C0J8G7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.52 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5 M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 53389 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Rmerge(I) obs: 0.1 / Rsym value: 0.101 / Net I/σ(I): 23.74
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 7.438 / Rsym value: 0.445 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→40.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.604 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20706 2711 5.1 %RANDOM
Rwork0.17715 ---
obs0.17868 50608 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0 Å2-0 Å2
2---0.5 Å2-0 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 18 518 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023150
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9534289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32125.697165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77915519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.465159
X-RAY DIFFRACTIONr_chiral_restr0.10.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212452
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 231 -
Rwork0.214 3632 -
obs--99.64 %

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