[English] 日本語
Yorodumi
- PDB-3o1x: High resolution crystal structure of histidine triad nucleotide-b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o1x
TitleHigh resolution crystal structure of histidine triad nucleotide-binding protein 1 (Hint1) C84A mutant from rabbit complexed with adenosine
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HINT PROTEIN / HIT PROTEIN / ADENOSINE 5'-MONOPHOSPHORAMIDASE
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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / proteolysis / nucleus / 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
ADENOSINE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsDolot, R.M. / Ozga, M. / Krakowiak, A.K. / Nawrot, B. / Stec, W.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Histidine Triad Nucleotide-binding Protein 1 (HINT-1) Phosphoramidase Transforms Nucleoside 5'-O-Phosphorothioates to Nucleoside 5'-O-Phosphates.
Authors: Ozga, M. / Dolot, R. / Janicka, M. / Kaczmarek, R. / Krakowiak, A.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9723
Polymers13,6821
Non-polymers2902
Water3,783210
1
A: Histidine triad nucleotide-binding protein 1
hetero molecules

A: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9446
Polymers27,3642
Non-polymers5804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5120 Å2
ΔGint-36 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.765, 39.765, 141.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase / P13.7


Mass: 13681.770 Da / Num. of mol.: 1 / Mutation: C84A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: HINT1, HINT / Plasmid: pSGA02 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P80912, Hydrolases
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 8000, 0.1M sodium cacodylate pH 6.5, O.1M sodium acetate, protein concentration 10 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 281K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 19, 2009 / Details: mirrors
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. obs: 49845 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.15
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.88 / Num. unique all: 2434 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
MAR345data collection
MOLREP10.2.31phasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LLJ

3llj
PDB Unreleased entry


Resolution: 1.08→23.05 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.815 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17139 2522 5.1 %RANDOM
Rwork0.14146 ---
all0.14296 49924 --
obs0.14296 47232 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.08→23.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 20 210 1113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211135
X-RAY DIFFRACTIONr_angle_refined_deg2.2721.9821562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68624.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56215195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.595154
X-RAY DIFFRACTIONr_chiral_restr0.1360.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021908
X-RAY DIFFRACTIONr_mcbond_it2.6641.5711
X-RAY DIFFRACTIONr_mcangle_it3.80821169
X-RAY DIFFRACTIONr_scbond_it4.8023424
X-RAY DIFFRACTIONr_scangle_it6.6844.5393
X-RAY DIFFRACTIONr_rigid_bond_restr2.58331135
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 189 -
Rwork0.303 3415 -
obs-3415 99.67 %

+
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