[English] 日本語
Yorodumi
- PDB-4h4f: Crystal structure of human chymotrypsin C (CTRC) bound to inhibit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h4f
TitleCrystal structure of human chymotrypsin C (CTRC) bound to inhibitor eglin c from Hirudo medicinalis
Components
  • (Chymotrypsin-C) x 2
  • Eglin C
Keywordshydrolase/hydrolase inhibitor / Serine protease / protease inhibitor / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


chymotrypsin C / Cobalamin (Cbl, vitamin B12) transport and metabolism / cobalamin metabolic process / serine-type endopeptidase inhibitor activity / response to wounding / intracellular calcium ion homeostasis / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 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. ...Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Eglin C / Chymotrypsin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBatra, J. / Soares, A.S. / Radisky, E.S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Long-range Electrostatic Complementarity Governs Substrate Recognition by Human Chymotrypsin C, a Key Regulator of Digestive Enzyme Activation.
Authors: Batra, J. / Szabo, A. / Caulfield, T.R. / Soares, A.S. / Sahin-Toth, M. / Radisky, E.S.
History
DepositionSep 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chymotrypsin-C
B: Eglin C
Q: Chymotrypsin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4426
Polymers37,1573
Non-polymers2853
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-36 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.272, 76.253, 81.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Chymotrypsin-C / Caldecrin


Mass: 28054.791 Da / Num. of mol.: 1 / Fragment: Chymotrypsin C (unp residues 30-268)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLCR, CTRC / Strain (production host): HEK 293T / References: UniProt: Q99895, chymotrypsin C
#2: Protein Eglin C


Mass: 8072.089 Da / Num. of mol.: 1 / Fragment: Eglin c (unp residues 8-70)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01051
#3: Protein/peptide Chymotrypsin-C / Caldecrin


Mass: 1030.197 Da / Num. of mol.: 1 / Fragment: CTRC propeptide (unp residues 17-26)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLCR, CTRC / Strain (production host): HEK 293T / References: UniProt: Q99895, chymotrypsin C
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN Q IS A PRO-DOMAIN THAT HAS BEEN CLEAVED UPON ACTIVATION BUT IT IS NOT RELEASED BECAUSE IT ...CHAIN Q IS A PRO-DOMAIN THAT HAS BEEN CLEAVED UPON ACTIVATION BUT IT IS NOT RELEASED BECAUSE IT MAKES A DISULPHIDE LINK

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M TRIS hydrochloride and 30 % (w/v) PEG 4000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→55.784 Å / Num. all: 27661 / Num. obs: 27661 / % possible obs: 97.34 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 51.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 9 / Rsym value: 0.146 / % possible all: 76.8

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementResolution: 1.9→55.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.753 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 1396 5 %RANDOM
Rwork0.1573 26265 --
obs0.1599 27661 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.52 Å2 / Biso mean: 25.5891 Å2 / Biso min: 12.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å20 Å20 Å2
2---2.95 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→55.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 15 320 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222552
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.9423484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27523.559118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80215395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7681517
X-RAY DIFFRACTIONr_chiral_restr0.1880.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211963
X-RAY DIFFRACTIONr_mcbond_it1.3811.51550
X-RAY DIFFRACTIONr_mcangle_it2.31922513
X-RAY DIFFRACTIONr_scbond_it3.61131002
X-RAY DIFFRACTIONr_scangle_it5.7484.5971
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 84 -
Rwork0.167 1534 -
all-1618 -
obs--77.68 %

+
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://pdbjlvh1.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