[English] 日本語
Yorodumi
- PDB-4l7w: Crystal structure mutant H77A of human HD domain-containing prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l7w
TitleCrystal structure mutant H77A of human HD domain-containing protein 2, Genomics Consortium (NESG) Target HR6723
ComponentsHD domain-containing protein 2
KeywordsSIGNALING PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HDCC2
Function / homology
Function and homology information


5'-deoxynucleotidase / 5'-deoxynucleotidase activity / metal ion binding
Similarity search - Function
HD domain / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5'-deoxynucleotidase HDDC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsKuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. ...Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR6723
Authors: Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Authors: Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionJun 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HD domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9336
Polymers23,8121
Non-polymers1225
Water79344
1
A: HD domain-containing protein 2
hetero molecules

A: HD domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,86612
Polymers47,6232
Non-polymers24310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455-x-1,-y,z1
Buried area5900 Å2
ΔGint-118 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.380, 71.380, 199.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

Detailsdimer,43.66 kD,73.0%|dimer,40.35 kD,20.3%

-
Components

#1: Protein HD domain-containing protein 2 / Hepatitis C virus NS5A-transactivated protein 2 / HCV NS5A-transactivated protein 2


Mass: 23811.594 Da / Num. of mol.: 1 / Mutation: H77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDDC2, C6orf74, NS5ATP2, CGI-130 / Plasmid: pET15_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7Z4H3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 8
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Mg(NO3)2, 0.1M Tris, 12% PEG 20000, microbatch under oil, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 11866 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 42.21 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 40.9

-
Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DMB

4dmb


Resolution: 2.305→35.69 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.2 / σ(F): 1.33 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 562 4.75 %
Rwork0.1739 --
obs0.1763 11843 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.794 Å2
Refinement stepCycle: LAST / Resolution: 2.305→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 5 44 1569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081544
X-RAY DIFFRACTIONf_angle_d1.1012080
X-RAY DIFFRACTIONf_dihedral_angle_d15.087604
X-RAY DIFFRACTIONf_chiral_restr0.073227
X-RAY DIFFRACTIONf_plane_restr0.004275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3045-2.53640.24121350.18572760X-RAY DIFFRACTION100
2.5364-2.90320.2451440.18732745X-RAY DIFFRACTION100
2.9032-3.65720.26431530.1892799X-RAY DIFFRACTION100
3.6572-35.69430.1981300.16072977X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -37.926 Å / Origin y: 10.2734 Å / Origin z: 8.7663 Å
111213212223313233
T0.5261 Å20.0441 Å20.0175 Å2-0.3129 Å20.0622 Å2--0.3179 Å2
L1.9497 °2-1.103 °2-0.5679 °2-3.6743 °20.333 °2--2.3721 °2
S0.3158 Å °0.4414 Å °0.2334 Å °-0.8404 Å °-0.2865 Å °-0.1672 Å °-0.3439 Å °0.0302 Å °-0.0059 Å °
Refinement TLS groupSelection details: all

+
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