[English] 日本語
Yorodumi
- PDB-1jrr: HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETIONMUT... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 2-Mercaptoethanol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more