[English] 日本語
Yorodumi
- PDB-8e5w: Crystal structure of dehydroalanine Hip1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8e5w
TitleCrystal structure of dehydroalanine Hip1
ComponentsProtease
KeywordsHYDROLASE / serine protease Hip1
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / proteolysis
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PALMITIC ACID / Protease
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGoldfarb, N.E. / Brooks, C.L. / Ostrov, D.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: 2.1 angstrom crystal structure of the Mycobacterium tuberculosis serine hydrolase, Hip1, in its anhydro-form (Anhydrohip1).
Authors: Brooks, C.L. / Ostrov, D.A. / Schumann, N.C. / Kakkad, S. / Li, D. / Pena, K. / Williams, B.P. / Goldfarb, N.E.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7825
Polymers52,2171
Non-polymers5654
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.891, 104.891, 127.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Protease


Mass: 52217.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tap, ERS007688_01841 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A654TLU9, Hydrolases; Acting on peptide bonds (peptidases), Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: ammonium sulfate PEG 8000 sodium cacodylate trihydrate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9436 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 44570 / % possible obs: 99.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 22.99 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.523 / Net I/σ(I): 7.7 / Num. measured all: 270167
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.15-2.195.40.56421811.439198.9
2.19-2.236.10.51521941.467199.1
2.23-2.276.10.46522021.469199.1
2.27-2.326.10.42921761.504199
2.32-2.376.10.38921981.495199.1
2.37-2.426.10.35721771.509199.3
2.42-2.486.10.31222171.518199.5
2.48-2.556.10.28122161.533199.5
2.55-2.626.10.26222061.543199.2
2.62-2.716.10.21822071.608199.5
2.71-2.816.10.18521951.553199.4
2.81-2.926.10.16122391.629199.5
2.92-3.056.10.13422141.615199.6
3.05-3.216.10.10722281.579199.7
3.21-3.416.10.08522451.569199.8
3.41-3.676.10.06822391.533199.8
3.67-4.046.10.05722721.56199.9
4.04-4.636.10.0522591.517199.9
4.63-5.8260.0523021.4191100
5.82-105.70.04324031.386199.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UNO

5uno


Resolution: 2.15→29.46 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 2248 5.05 %
Rwork0.16 42297 -
obs0.1615 44545 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.73 Å2 / Biso mean: 30.0853 Å2 / Biso min: 12.95 Å2
Refinement stepCycle: final / Resolution: 2.15→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 88 542 4160
Biso mean--45.44 35.02 -
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20.23191520.18822574272699
2.2-2.250.20341390.17922596273599
2.25-2.30.21051470.17092587273499
2.3-2.370.19521330.16152624275799
2.37-2.430.20291500.16342603275399
2.44-2.510.20251410.16062583272499
2.51-2.60.19591280.157626272755100
2.6-2.710.19921290.1572661279099
2.71-2.830.17931350.160426342769100
2.83-2.980.1941580.163226022760100
2.98-3.170.19411320.15626612793100
3.17-3.410.19291450.159426522797100
3.41-3.750.1831430.142226622805100
3.75-4.290.15111210.136826992820100
4.3-5.40.17341530.147627042857100
5.41-29.460.20421420.200428282970100
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)
11.75820.11420.32321.99270.47473.2403-0.07730.14640.3225-0.23280.07620.24680.0097-0.25750.00720.1995-0.0643-0.0570.17730.06440.276920.4117-27.7591-10.6093
21.30740.82620.34780.81430.0380.43320.0042-0.11180.11670.0381-0.02020.16010.0253-0.12710.01780.1862-0.012-0.00380.1847-0.01590.188331.7953-29.50532.9819
36.64032.5546-5.76630.9273-2.31444.9343-0.0099-0.1267-0.11370.0201-0.04870.00940.25980.10230.09560.25050.0026-0.00130.15260.02220.188551.0228-40.715-4.4345
41.2663-0.1124-0.2852.93671.872.1376-0.04110.05240.0765-0.0180.0614-0.2067-0.03810.2881-0.00290.1631-0.02080.01420.15750.04690.145361.8098-25.8421-5.0385
51.61160.063-0.86680.63010.111.8025-0.0010.04980.0963-0.1134-0.06180.0555-0.023-0.02820.06140.1724-0.0143-0.03140.12820.00190.14746.6421-25.9881-5.8092
61.0958-0.2795-0.85243.66640.71085.7259-0.088-0.1113-0.21190.1952-0.0202-0.08520.55370.06220.13470.1961-0.0172-0.01160.12910.03930.158754.0258-35.873110.4532
71.29720.20180.18670.9842-0.06780.93910.01860.0391-0.1732-0.12520.02790.01530.2314-0.0971-0.03790.2269-0.0523-0.00440.15040.00160.185832.4777-44.9674-6.644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 149 )A44 - 149
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 259 )A150 - 259
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 284 )A260 - 284
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 329 )A285 - 329
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 401 )A330 - 401
6X-RAY DIFFRACTION6chain 'A' and (resid 402 through 431 )A402 - 431
7X-RAY DIFFRACTION7chain 'A' and (resid 432 through 520 )A432 - 520

+
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