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- PDB-2arq: Human plasminogen activator inhibitor-2.[loop (66-98) deletion mu... -

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Basic information

Entry
Database: PDB / ID: 2arq
TitleHuman plasminogen activator inhibitor-2.[loop (66-98) deletion mutant] complexed with peptide n-acetyl-teaaagdggvmtgr-oh
Components
  • 14-mer from Plasminogen activator inhibitor-2
  • Plasminogen activator inhibitor-2
Keywordshydrolase inhibitor/peptide / SERPIN / PEPTIDE BINDING / inhibitor / hydrolase inhibitor-peptide complex
Function / homology
Function and homology information


cornified envelope / Dissolution of Fibrin Clot / fibrinolysis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / serine-type endopeptidase inhibitor activity / negative regulation of apoptotic process / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Plasminogen activator inhibitor-2 / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Plasminogen activator inhibitor-2 / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Plasminogen activator inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDi Giusto, D.A. / Sutherland, A.P. / Jankova, L. / Harrop, S.J. / Curmi, P.M. / King, G.C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Plasminogen activator inhibitor-2 is highly tolerant to P8 residue substitution--implications for serpin mechanistic model and prediction of nsSNP activities
Authors: Di Giusto, D.A. / Sutherland, A.P. / Jankova, L. / Harrop, S.J. / Curmi, P.M. / King, G.C.
History
DepositionAug 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasminogen activator inhibitor-2
P: 14-mer from Plasminogen activator inhibitor-2


Theoretical massNumber of molelcules
Total (without water)44,3062
Polymers44,3062
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-10 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.562, 104.126, 41.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Plasminogen activator inhibitor-2 / PAI-2 / Placental plasminogen activator inhibitor / Monocyte Arg-serpin / Urokinase inhibitor


Mass: 42986.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05120
#2: Protein/peptide 14-mer from Plasminogen activator inhibitor-2 / PAI-2 / Placental plasminogen activator inhibitor / Monocyte Arg-serpin / Urokinase inhibitor


Mass: 1319.423 Da / Num. of mol.: 1 / Mutation: T373D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05120
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Oct 9, 1999 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→14.8 Å / Num. all: 33539 / Num. obs: 33539 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 15.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3330 / Rsym value: 0.417 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JRR

1jrr


Resolution: 1.85→14.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.491 / SU ML: 0.107 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24822 1061 3.2 %RANDOM
Rwork0.18246 ---
all0.18469 32455 --
obs0.18469 32455 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---1.28 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 1.85→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 0 345 3314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223056
X-RAY DIFFRACTIONr_bond_other_d0.0010.022744
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9654121
X-RAY DIFFRACTIONr_angle_other_deg0.87536411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47524.397141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01915550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5321516
X-RAY DIFFRACTIONr_chiral_restr0.1060.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
X-RAY DIFFRACTIONr_nbd_refined0.210.2583
X-RAY DIFFRACTIONr_nbd_other0.1920.22692
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21420
X-RAY DIFFRACTIONr_nbtor_other0.0880.21773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.219
X-RAY DIFFRACTIONr_mcbond_it1.5241.52414
X-RAY DIFFRACTIONr_mcbond_other0.3231.5766
X-RAY DIFFRACTIONr_mcangle_it1.84423015
X-RAY DIFFRACTIONr_scbond_it2.88831383
X-RAY DIFFRACTIONr_scangle_it3.9994.51102
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 72 -
Rwork0.258 2371 -
obs--96.48 %

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