[English] 日本語
Yorodumi
- PDB-5iz5: Human GIVD cytosolic phospholipase A2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iz5
TitleHuman GIVD cytosolic phospholipase A2
ComponentsCytosolic phospholipase A2 delta
KeywordsHYDROLASE / Signal Transduction / Phospholipase / alpha/beta hydrolase / Calcium binding / C2 domain
Function / homology
Function and homology information


phosphatidylglycerol acyl-chain remodeling / phosphatidylinositol acyl-chain remodeling / glycerophospholipid catabolic process / Hydrolysis of LPC / Acyl chain remodelling of PG / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE ...phosphatidylglycerol acyl-chain remodeling / phosphatidylinositol acyl-chain remodeling / glycerophospholipid catabolic process / Hydrolysis of LPC / Acyl chain remodelling of PG / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / calcium-dependent phospholipid binding / phospholipase A2 / calcium-dependent phospholipase A2 activity / fatty acid metabolic process / calcium ion binding / membrane / cytosol
Similarity search - Function
Cytosolic phospholipases A2, C2-domain / Cytosolic phospholipases A2 C2-domain / Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / Acyl transferase/acyl hydrolase/lysophospholipase / Protein kinase C conserved region 2 (CalB) / C2 domain ...Cytosolic phospholipases A2, C2-domain / Cytosolic phospholipases A2 C2-domain / Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / Acyl transferase/acyl hydrolase/lysophospholipase / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Cytosolic phospholipase A2 delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsWang, H. / Klein, M.G.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition.
Authors: Wang, H. / Klein, M.G. / Snell, G. / Lane, W. / Zou, H. / Levin, I. / Li, K. / Sang, B.C.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Cytosolic phospholipase A2 delta
A: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,91316
Polymers182,5682
Non-polymers1,34514
Water7,782432
1
A: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6685
Polymers91,2841
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,24511
Polymers91,2841
Non-polymers96110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.783, 180.783, 133.539
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 16 - 807 / Label seq-ID: 20 - 811

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

-
Components

#1: Protein Cytosolic phospholipase A2 delta / cPLA2-delta / Phospholipase A2 group IVD


Mass: 91284.094 Da / Num. of mol.: 2 / Fragment: UNP residues 2-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G4D / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86XP0, phospholipase A2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris-propane (pH 7.0-7.5), 1.4-1.5 M Lithium Sulphate
PH range: 7.0-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→156.56 Å / Num. obs: 125039 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→156.56 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.811 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23781 6279 5 %RANDOM
Rwork0.22322 ---
obs0.22394 118594 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→156.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11958 0 70 432 12460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912414
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211649
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.97816857
X-RAY DIFFRACTIONr_angle_other_deg1326850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9351511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50123.857586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.772152090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6421591
X-RAY DIFFRACTIONr_chiral_restr0.070.21856
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113961
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022854
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_it1.955.4656065
X-RAY DIFFRACTIONr_mcbond_other1.955.4646064
X-RAY DIFFRACTIONr_mcangle_it3.3088.1837569
X-RAY DIFFRACTIONr_mcangle_other3.3088.1847570
X-RAY DIFFRACTIONr_scbond_it2.0055.7376348
X-RAY DIFFRACTIONr_scbond_other1.9865.7126293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3678.4739205
X-RAY DIFFRACTIONr_long_range_B_refined6.4442.85813872
X-RAY DIFFRACTIONr_long_range_B_other6.39242.83713738
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 39149 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 434 -
Rwork0.312 8562 -
obs--97.63 %

+
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