[English] 日本語
Yorodumi
- PDB-2r0k: Protease domain of HGFA with inhibitor Fab58 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r0k
TitleProtease domain of HGFA with inhibitor Fab58
Components
  • Hepatocyte growth factor activator
  • antibody heavy chain of Fab58, Fab portion only
  • antibody light chain of Fab58
KeywordsHYDROLASE / IMMUNE SYSTEM / serine protease / antibody / inhibitor / EGF-like domain / Glycoprotein / Kringle / Secreted / Zymogen
Function / homology
Function and homology information


MET Receptor Activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / rough endoplasmic reticulum / serine-type peptidase activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol
Similarity search - Function
Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. ...Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsEigenbrot, C. / Shia, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural insight into distinct mechanisms of protease inhibition by antibodies.
Authors: Wu, Y. / Eigenbrot, C. / Liang, W.C. / Stawicki, S. / Shia, S. / Fan, B. / Ganesan, R. / Lipari, M.T. / Kirchhofer, D.
History
DepositionAug 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 5, 2014Group: Source and taxonomy
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hepatocyte growth factor activator
L: antibody light chain of Fab58
H: antibody heavy chain of Fab58, Fab portion only


Theoretical massNumber of molelcules
Total (without water)77,8613
Polymers77,8613
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.658, 75.610, 69.139
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Hepatocyte growth factor activator


Mass: 30885.154 Da / Num. of mol.: 1 / Fragment: HGFA protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGFAC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Antibody antibody light chain of Fab58


Mass: 23287.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The protein was made using a synthetically diversified gene library and selected for tight binding to a specific target on a plastic surface. The gene library used cloned human genes as its basis
Production host: Escherichia coli (E. coli)
#3: Antibody antibody heavy chain of Fab58, Fab portion only


Mass: 23688.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The protein was made using a synthetically diversified gene library and selected for tight binding to a specific target on a plastic surface. The gene library used cloned human genes as its basis.
Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 9.5
Details: 1:1 mixture of protein complex solution and reservoir containing 1.0M K/Na tartrate, CHES pH9.5, 0.2M Lithium Sulfate, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2007
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 10827 / Num. obs: 10827 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.8 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 6.8
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / % possible all: 85.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 1YBW, pdb 1FVD

1ybw

1fvd


Resolution: 3.51→50 Å / Cor.coef. Fo:Fc: 0.83 / Cor.coef. Fo:Fc free: 0.746 / SU B: 81.71 / SU ML: 0.585 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -2 / ESU R Free: 0.813 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31197 526 4.9 %RANDOM
Rwork0.25056 ---
all0.254 10827 --
obs0.25354 10827 87.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.411 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å22.9 Å2
2---0.39 Å20 Å2
3---2.26 Å2
Refinement stepCycle: LAST / Resolution: 3.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 0 0 5042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225174
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9497051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58423.793203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89915787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.681522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023937
X-RAY DIFFRACTIONr_nbd_refined0.2190.22321
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4620.21
X-RAY DIFFRACTIONr_mcbond_it1.9072.53371
X-RAY DIFFRACTIONr_mcangle_it3.27655339
X-RAY DIFFRACTIONr_scbond_it1.5442.52064
X-RAY DIFFRACTIONr_scangle_it2.46351712
LS refinement shellResolution: 3.508→3.599 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 45 -
Rwork0.255 675 -
obs--81.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5155-1.2845-1.18531.7346-0.30930.83520.22350.04330.21030.04410.09810.0004-0.18980.1477-0.32160.0339-0.05670.0012-0.0933-0.0019-0.068420.030511.224712.6755
22.45851.2982-1.06082.9899-1.08040.98770.09360.15570.1850.430.16360.0142-0.2971-0.3296-0.25720.04470.04450.0656-0.04550.0556-0.1285-13.610913.455825.6033
31.25340.0165-1.35450.479-0.00441.4641-0.1447-0.0867-0.1596-0.03830.11920.03510.06530.03940.0255-0.02560.03260.0233-0.07650.00280.061316.4592-10.629917.4815
42.9689-0.17290.50923.2057-0.84310.2944-0.17770.09370.0134-0.25130.1577-0.23280.0971-0.34830.02-0.0015-0.00210.00040.00930.0262-0.1727-13.82680.468416.2427
51.5302-0.8387-0.25081.42940.02720.64040.0414-0.0183-0.0286-0.02930.00540.00010.0029-0.0018-0.0468-0.0811-0.00210.0171-0.0878-0.01110.015844.1627-18.76982.8051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LB1 - 1071 - 107
2X-RAY DIFFRACTION2LB108 - 214108 - 214
3X-RAY DIFFRACTION3HC1 - 1191 - 123
4X-RAY DIFFRACTION4HC120 - 216124 - 220
5X-RAY DIFFRACTION5AA16 - 24336 - 274

+
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