[English] 日本語
Yorodumi
- PDB-5uvm: HIT family hydrolase from Clostridium thermocellum Cth-393 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uvm
TitleHIT family hydrolase from Clostridium thermocellum Cth-393
ComponentsHistidine triad (HIT) protein
KeywordsHYDROLASE / Southeast Collaboratory for Structural Genomics / SECSG / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
Scavenger mRNA decapping enzyme C-term binding / Histidine triad (HIT) protein / 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 / Histidine triad (HIT) protein
Similarity search - Component
Biological speciesRuminiclostridium thermocellum DSM 1313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsHabel, J. / Tempel, W. / Liu, Z.-J. / Rose, J. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To Be Published
Title: HIT family hydrolase from Clostridium thermocellum Cth-393
Authors: Habel, J. / Tempel, W. / Liu, Z.-J. / Rose, J. / Wang, B.-C.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionApr 5, 2017ID: 1XQU
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Oct 4, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 15, 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: Histidine triad (HIT) protein
B: Histidine triad (HIT) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,20336
Polymers32,7772
Non-polymers2,42634
Water50428
1
A: Histidine triad (HIT) protein
hetero molecules

A: Histidine triad (HIT) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,26340
Polymers32,7772
Non-polymers2,48638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area3310 Å2
ΔGint-23 kcal/mol
Surface area10140 Å2
MethodPISA
2
B: Histidine triad (HIT) protein
hetero molecules

B: Histidine triad (HIT) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,14332
Polymers32,7772
Non-polymers2,36630
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x,-y+1,-z-1/21
Buried area4320 Å2
ΔGint-24 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.804, 78.804, 114.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein Histidine triad (HIT) protein


Mass: 16388.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum DSM 1313 (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_1369 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DF72
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 65.409 Da / Num. of mol.: 31 / Source method: obtained synthetically
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3000, 0.2M sodium chloride, 0.1M HEPES, pH 7.5

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.969 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 16265 / % possible obs: 98 %

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1XQU

1xqu
PDB Unreleased entry


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.343 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.187
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Metal ions were assigned as zinc based on amino acid residue types at the binding site and following precedence of PDB entries 4EGU, 3OJ7, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Metal ions were assigned as zinc based on amino acid residue types at the binding site and following precedence of PDB entries 4EGU, 3OJ7, 3OMF. CAUTION: The ligand bound near Asp30 of chain B was tentatively identified as adenosine based on the shape of difference electron density and the presence of similar ligands in PDB entries 4EGU, 3OMF. Ultimate identity and origin of the ligand remain unknown. There is similar but weaker electron density near an equivalent site in chain A. Restraints for adenosine geometry were prepared on the GRADE server (GLOBALPHASING). We note the dubious fit of the Leu1 side chain to electron density and suspect a misassignment or mutation of this residue.
RfactorNum. reflection% reflectionSelection details
Rfree0.23292 495 3.1 %FLAGS TAKEN FROM PDB ENTRY 1XQU
Rwork0.20597 ---
obs0.20678 15683 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 52 28 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191823
X-RAY DIFFRACTIONr_bond_other_d0.0020.021719
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9642492
X-RAY DIFFRACTIONr_angle_other_deg1.0463.0023976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7982572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25515294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.331156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212070
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02324
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9394.102925
X-RAY DIFFRACTIONr_mcbond_other2.9324.1924
X-RAY DIFFRACTIONr_mcangle_it4.3546.1391155
X-RAY DIFFRACTIONr_mcangle_other4.3566.1411156
X-RAY DIFFRACTIONr_scbond_it3.2594.303898
X-RAY DIFFRACTIONr_scbond_other3.2574.303898
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0146.341334
X-RAY DIFFRACTIONr_long_range_B_refined6.56647.9421933
X-RAY DIFFRACTIONr_long_range_B_other6.56147.9281931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 33 -
Rwork0.256 1112 -
obs--95.1 %

+
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