[English] 日本語
Yorodumi
- PDB-4eqe: Crystal structure of histidine triad nucleotide-binding protein 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eqe
TitleCrystal structure of histidine triad nucleotide-binding protein 1 (HINT1) from human complexed with Lys-AMS
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HIT domain
Function / homology
Function and homology information


purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsWang, J. / Fang, P. / Guo, M.
CitationJournal: J.Phys.Chem.B / Year: 2012
Title: Side chain independent recognition of aminoacyl adenylates by the hint1 transcription suppressor.
Authors: Wang, J. / Fang, P. / Schimmel, P. / Guo, M.
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7614
Polymers28,0482
Non-polymers7132
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-12 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.001, 46.409, 64.225
Angle α, β, γ (deg.)90.000, 95.460, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-201-

EPE

-
Components

#1: Protein Histidine triad nucleotide-binding protein 1 / HINT1 / Adenosine 5'-monophosphoramidase


Mass: 14024.165 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT / Production host: Escherichia coli (E. coli) / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N8O7S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25-28% PEG3350, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.52→25 Å / Num. obs: 35542 / % possible obs: 99.3 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.048 / Χ2: 0.952 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.52-1.576.50.29934610.869198.2
1.57-1.647.50.24135390.896198.7
1.64-1.717.60.18334830.904198.7
1.71-1.87.60.13535320.923199
1.8-1.917.60.09735490.97199.5
1.91-2.067.60.07735451.196199.5
2.06-2.277.60.05835681.122199.8
2.27-2.67.60.04435740.95199.9
2.6-3.277.60.03936261.0811100
3.27-257.40.02636650.592199.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6RHN

6rhn


Resolution: 1.52→24.396 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.9199 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 14.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1622 1739 5 %
Rwork0.1421 --
obs0.1431 34771 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.794 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 59.82 Å2 / Biso mean: 16.5139 Å2 / Biso min: 5.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.2044 Å2-0 Å20.7151 Å2
2--0.2432 Å20 Å2
3----0.0388 Å2
Refinement stepCycle: LAST / Resolution: 1.52→24.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 37 291 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081898
X-RAY DIFFRACTIONf_angle_d1.1892590
X-RAY DIFFRACTIONf_chiral_restr0.084285
X-RAY DIFFRACTIONf_plane_restr0.005334
X-RAY DIFFRACTIONf_dihedral_angle_d15.273717
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.52-1.56480.21451070.18532207231479
1.5648-1.61530.18741530.1652606275992
1.6153-1.6730.18021410.1522732287398
1.673-1.740.19341350.1442794292999
1.74-1.81920.16751420.13932839298199
1.8192-1.9150.16541550.13232788294399
1.915-2.0350.1521560.12862790294699
2.035-2.1920.1861420.144428432985100
2.192-2.41240.15681430.13728412984100
2.4124-2.76110.15911520.148628232975100
2.7611-3.47710.15461630.134328493012100
3.4771-24.39910.14851500.143429203070100
Refinement TLS params.Method: refined / Origin x: 23.5667 Å / Origin y: -0.0215 Å / Origin z: 15.924 Å
111213212223313233
T0.0488 Å2-0.0025 Å2-0.0096 Å2-0.0354 Å20.0026 Å2--0.0603 Å2
L0.3173 °2-0.0114 °20.009 °2-0.8457 °20.1113 °2--1.3918 °2
S0.005 Å °-0.0226 Å °-0.0164 Å °-0.0119 Å °0.0002 Å °-0.0291 Å °0.0571 Å °0.0318 Å °0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 344
2X-RAY DIFFRACTION1allB12 - 447

+
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