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- PDB-1jrr: HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETIONMUT... -

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Basic information

Entry
Database: PDB / ID: 1jrr
TitleHUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETIONMUTANT] COMPLEXED WITH PEPTIDE MIMIckING THE REACTIVE CENTER LOOP
Components(PLASMINOGEN ACTIVATOR INHIBITOR-2) x 2
KeywordsPEPTIDE BINDING PROTEIN / SERPIN / PEPTIDE BINDING
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
BETA-MERCAPTOETHANOL / Plasminogen activator inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJankova, L. / Harrop, S.J. / Saunders, D.N. / Andrews, J.L. / Bertram, K.C. / Gould, A.R. / Baker, M.S. / Curmi, P.M.G.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: CRYSTAL STRUCTURE OF THE COMPLEX OF PLASMINOGEN ACTIVATOR INHIBITOR 2 WITH A PEPTIDE MIMICKING THE REACTIVE CENTER LOOP
Authors: JANKOVA, L. / HARROP, S.J. / SAUNDERS, D.N. / ANDREWS, J.L. / BERTRAM, K.C. / GOULD, A.R. / BAKER, M.S. / CURMI, P.M.G.
#1: Journal: To be Published
Title: INTERACTION BETWEEN THE P14 RESIDUE AND STRAND 2 OF BETA-SHEET B IS CRITICAL FOR REACTIVE CENTER LOOP INSERTION IN PAI-2
Authors: SAUNDERS, D.N. / GOULD, A.R. / RANSON, M. / JANKOVA, L. / HARROP, S.J. / G CURMI, P.M. / BAKER, M.S.
History
DepositionAug 15, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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 / _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: PLASMINOGEN ACTIVATOR INHIBITOR-2
P: PLASMINOGEN ACTIVATOR INHIBITOR-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4293
Polymers44,3502
Non-polymers781
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-15 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.139, 104.160, 41.395
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


Mass: 43045.020 Da / Num. of mol.: 1 / Mutation: RESIDUES 66 - 98 EXCISED
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 PLASMINOGEN ACTIVATOR INHIBITOR-2


Mass: 1305.439 Da / Num. of mol.: 1 / Fragment: RESIDUES 367-380 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P05120
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
25 mMHEPES1drop
3100 mM1dropNaCl
413 %PEG80001reservoir
50.1 Mmagnesium acetate1reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→69.01 Å / Num. all: 313356 / Num. obs: 49516 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.049 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3 / Rsym value: 0.22 / % possible all: 74.6
Reflection
*PLUS
Num. measured all: 313356 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 74.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→69.01 Å / SU B: 2.5 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.098 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22529 1596 3.1 %RANDOM
Rwork0.19725 ---
all0.19531 51189 --
obs0.19815 49516 94.6 %-
Displacement parametersBiso mean: 17.156 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.68 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.6→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 0 442 3419
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9111.5
X-RAY DIFFRACTIONp_mcangle_it1.7062
X-RAY DIFFRACTIONp_scbond_it2.5713
X-RAY DIFFRACTIONp_scangle_it4.0944.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellHighest resolution: 1.6 Å / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.224 / Total num. of bins used: 20
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.2

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