[English] 日本語
Yorodumi
- PDB-4l8y: Crystal structure of gamma-glutamyl hydrolase (C108A) from zebrafish -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l8y
TitleCrystal structure of gamma-glutamyl hydrolase (C108A) from zebrafish
ComponentsGamma-glutamyl hydrolase
KeywordsHYDROLASE / Sandwiched-like domain
Function / homology
Function and homology information


folate gamma-glutamyl hydrolase / tetrahydrofolylpolyglutamate metabolic process / gamma-glutamyl-peptidase activity / Neutrophil degranulation / folic acid-containing compound metabolic process / vacuole / extracellular region
Similarity search - Function
Peptidase C26, gamma-glutamyl hydrolase / Gamma-glutamyl hydrolase domain profile. / Peptidase C26 / Peptidase C26 / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
folate gamma-glutamyl hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsChuankhayan, P. / Kao, T.-T. / Chen, C.-J. / Fu, T.-F.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural insights into the hydrolysis and polymorphism of methotrexate polyglutamate by zebrafish gamma-glutamyl hydrolase
Authors: Chuankhayan, P. / Kao, T.-T. / Lin, C.-C. / Guan, H.-H. / Nakagawa, A. / Fu, T.-F. / Chen, C.-J.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Gamma-glutamyl hydrolase
D: Gamma-glutamyl hydrolase
A: Gamma-glutamyl hydrolase
B: Gamma-glutamyl hydrolase


Theoretical massNumber of molelcules
Total (without water)141,5404
Polymers141,5404
Non-polymers00
Water15,565864
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Gamma-glutamyl hydrolase
D: Gamma-glutamyl hydrolase


Theoretical massNumber of molelcules
Total (without water)70,7702
Polymers70,7702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-12 kcal/mol
Surface area22530 Å2
MethodPISA
3
A: Gamma-glutamyl hydrolase
B: Gamma-glutamyl hydrolase


Theoretical massNumber of molelcules
Total (without water)70,7702
Polymers70,7702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-10 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.586, 206.505, 65.198
Angle α, β, γ (deg.)90.00, 113.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Gamma-glutamyl hydrolase


Mass: 35384.898 Da / Num. of mol.: 4 / Mutation: C108A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ggh / Production host: Escherichia coli (E. coli)
References: UniProt: Q6NY42, folate gamma-glutamyl hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20%(w/v) PEG 8000, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. all: 87110 / Num. obs: 87110 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.97→2 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
X-PLORmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9X

1l9x


Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.887 / SU B: 4.696 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25779 4361 5 %RANDOM
Rwork0.19878 ---
all0.21 82658 --
obs0.20177 82658 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.52 Å2
2--0.45 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9232 0 0 864 10096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229492
X-RAY DIFFRACTIONr_angle_refined_deg2.0811.95112887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91751144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35724.222450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.252151543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2051536
X-RAY DIFFRACTIONr_chiral_restr0.1790.21380
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217325
X-RAY DIFFRACTIONr_mcbond_it1.2211.55736
X-RAY DIFFRACTIONr_mcangle_it2.08129273
X-RAY DIFFRACTIONr_scbond_it3.25333756
X-RAY DIFFRACTIONr_scangle_it4.9624.53614
LS refinement shellResolution: 1.974→2.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 306 -
Rwork0.218 5847 -
obs--96.68 %

+
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