[English] 日本語
Yorodumi
- PDB-3zi1: Crystal structure of human glyoxalase domain-containing protein 4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zi1
TitleCrystal structure of human glyoxalase domain-containing protein 4 (GLOD4)
ComponentsGLYOXALASE DOMAIN-CONTAINING PROTEIN 4
KeywordsISOMERASE
Function / homology
Function and homology information


cadherin binding / mitochondrion / extracellular exosome
Similarity search - Function
Glyoxalase domain-containing protein 4 / Glyoxalase domain-containing protein 4, C-terminal / Glyoxalase domain-containing protein 4, N-terminal / Glyoxalasedomain-containing protein 4-like, C-terminal domain / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Glyoxalase domain-containing protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOberholzer, A. / Kiyani, W. / Shrestha, L. / Vollmar, M. / Krojer, T. / Froese, D.S. / Williams, E. / von Delft, F. / Burgess-Brown, N. / Arrowsmith, C.H. ...Oberholzer, A. / Kiyani, W. / Shrestha, L. / Vollmar, M. / Krojer, T. / Froese, D.S. / Williams, E. / von Delft, F. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of Human Glyoxalase Domain- Containing Protein 4 (Glod4)
Authors: Oberholze, A. / Kiyani, W. / Shrestha, L. / Vollmar, M. / Krojer, T. / Froese, D.S. / Williams, E. / von Delft, F. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionDec 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GLYOXALASE DOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1575
Polymers36,9091
Non-polymers2484
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.291, 42.918, 68.103
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein GLYOXALASE DOMAIN-CONTAINING PROTEIN 4


Mass: 36908.668 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-272 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9HC38
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN TERMINAL MHHHHHHSSGVDLGTENLYFQS DUE TO UNCLEAVED PURIFICATION TAG AND C TERMINAL ...N TERMINAL MHHHHHHSSGVDLGTENLYFQS DUE TO UNCLEAVED PURIFICATION TAG AND C TERMINAL NCWIDSKGGYGSEFELRRQACGRTRAPPPPPLRSGC DUE TO DNA FRAME SHIFT AS A RESULT OF CLONING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.11 % / Description: NONE
Crystal growDetails: 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH 7.5, 25%(W/V) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.89→68.1 Å / Num. obs: 27935 / % possible obs: 98.2 % / Observed criterion σ(I): 2.2 / Redundancy: 4.4 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 1.89→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.2 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FA8

1fa8


Resolution: 1.9→119.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.804 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20398 1419 5.1 %RANDOM
Rwork0.16511 ---
obs0.16713 26497 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.639 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→119.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 16 367 2534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9613048
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8424.587109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27815378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7981512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211731
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 107 -
Rwork0.234 1770 -
obs--96.7 %
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)
11.10.2822-0.4640.42480.05360.47620.016-0.0760.05280.010.0168-0.03330.06010.0118-0.03280.04440.00160.00870.0263-0.00540.017245.30875.21816.7997
22.9119-2.5443-2.81232.31082.2763.6868-0.0212-0.2340.2760.07340.1156-0.3354-0.20630.3192-0.09440.149-0.0458-0.03730.16310.04530.146242.38838.822228.0464
30.62490.14470.03330.65570.08570.96010.03080.0146-0.00330.0062-0.00190.00120.0571-0.0961-0.02880.0278-0.00270.00630.01240.00010.009935.85843.27210.7849
40.88390.42880.01830.9579-0.28510.1331-0.01450.1233-0.0098-0.0820.0169-0.08330.0120.0175-0.00230.05260.00880.02510.02050.00220.070245.850712.54322.7751
53.54810.29670.27291.00650.67940.46780.03720.33020.0592-0.157-0.0447-0.0242-0.1074-0.01830.00750.0580.01510.0160.05650.02380.063846.981417.3978-2.8327
61.54170.0823-0.43040.5158-0.06970.34230.0377-0.04420.00160.00810.00380.0037-0.04670.0302-0.04150.03330.00840.01260.0134-0.01360.045345.11615.2728.6904
74.1928-6.20241.296215.1257-5.01592.06680.0865-0.30440.48990.0865-0.0847-0.5139-0.10750.1611-0.00170.0361-0.01590.00820.0784-0.04110.131661.194523.905615.4794
80.8592-0.0769-0.29771.4755-0.47380.47780.1087-0.18810.12270.111-0.0801-0.0592-0.08840.1227-0.02860.0409-0.0232-0.00590.0562-0.03410.037553.710716.427819.7983
99.42943.6848-2.9134.7649-0.15662.2777-0.4102-0.523-1.20390.1554-0.0165-0.56440.34990.0790.42670.13540.04710.01620.11480.05610.187246.1509-6.074224.0008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 37
2X-RAY DIFFRACTION2A38 - 59
3X-RAY DIFFRACTION3A60 - 120
4X-RAY DIFFRACTION4A129 - 157
5X-RAY DIFFRACTION5A158 - 176
6X-RAY DIFFRACTION6A177 - 207
7X-RAY DIFFRACTION7A208 - 220
8X-RAY DIFFRACTION8A221 - 264
9X-RAY DIFFRACTION9A265 - 277

+
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