[English] 日本語
Yorodumi
- PDB-4bc7: MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: Arg419His mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bc7
TitleMAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: Arg419His mutant
ComponentsALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
KeywordsTRANSFERASE / PLASMALOGEN / FLAVIN / PEROXISOME
Function / homology
Function and homology information


alkylglycerone-phosphate synthase / alkylglycerone-phosphate synthase activity / ether lipid biosynthetic process / peroxisomal membrane / FAD binding / peroxisome
Similarity search - Function
Double Stranded RNA Binding Domain - #650 / GMP Synthetase; Chain A, domain 3 - #330 / Alpha-Beta Plaits - #3450 / Alkyldihydroxyacetonephosphate synthase / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal ...Double Stranded RNA Binding Domain - #650 / GMP Synthetase; Chain A, domain 3 - #330 / Alpha-Beta Plaits - #3450 / Alkyldihydroxyacetonephosphate synthase / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / GMP Synthetase; Chain A, domain 3 / Double Stranded RNA Binding Domain / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1-DODECANOL / FLAVIN-ADENINE DINUCLEOTIDE / Alkyldihydroxyacetonephosphate synthase, peroxisomal
Similarity search - Component
Biological speciesCAVIA PORCELLUS (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNenci, S. / Piano, V. / Rosati, S. / Aliverti, A. / Pandini, V. / Fraaije, M.W. / Heck, A.J.R. / Edmondson, D.E. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Precursor of Ether Phospholipids is Synthesized by a Flavoenzyme Through Covalent Catalysis.
Authors: Nenci, S. / Piano, V. / Rosati, S. / Aliverti, A. / Pandini, V. / Fraaije, M.W. / Heck, A.J.R. / Edmondson, D.E. / Mattevi, A.
History
DepositionOct 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 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_ncs_dom_lim / 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_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 / _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: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,38612
Polymers291,6794
Non-polymers3,7078
Water2,900161
1
A: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6936
Polymers145,8392
Non-polymers1,8534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-63 kcal/mol
Surface area38790 Å2
MethodPISA
2
C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6936
Polymers145,8392
Non-polymers1,8534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-63.1 kcal/mol
Surface area38620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.410, 99.190, 107.460
Angle α, β, γ (deg.)90.58, 91.88, 95.03
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYSAA81 - 10281 - 102
21GLYGLYLYSLYSBB81 - 10281 - 102
31GLYGLYLYSLYSCC81 - 10281 - 102
41GLYGLYLYSLYSDD81 - 10281 - 102
12SERSERARGARGAA158 - 265158 - 265
22SERSERARGARGBB158 - 265158 - 265
32SERSERARGARGCC158 - 265158 - 265
42SERSERARGARGDD158 - 265158 - 265
13VALVALGLNGLNAA278 - 425278 - 425
23VALVALGLNGLNBB278 - 425278 - 425
33VALVALGLNGLNCC278 - 425278 - 425
43VALVALGLNGLNDD278 - 425278 - 425
14VALVALGLYGLYAA465 - 472465 - 472
24VALVALGLYGLYBB465 - 472465 - 472
34VALVALGLYGLYCC465 - 472465 - 472
44VALVALGLYGLYDD465 - 472465 - 472
15METMETTYRTYRAA514 - 578514 - 578
25METMETTYRTYRBB514 - 578514 - 578
35METMETTYRTYRCC514 - 578514 - 578
45METMETTYRTYRDD514 - 578514 - 578
16VALVALLEULEUAA594 - 658594 - 658
26VALVALLEULEUBB594 - 658594 - 658
36VALVALLEULEUCC594 - 658594 - 658
46VALVALLEULEUDD594 - 658594 - 658

-
Components

#1: Protein
ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL / ALKYL-DHAP SYNTHASE / ALKYLGLYCERONE-PHOSPHATE SYNTHASE


Mass: 72919.648 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAVIA PORCELLUS (domestic guinea pig) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P97275, alkylglycerone-phosphate synthase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1DO / 1-DODECANOL


Mass: 186.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.23 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CRYSTALS WERE OBTAINED USING VAPOR-DIFFUSION SITTING-DROP AT 20 DEGREES C BY MIXING EQUAL VOLUMES OF 10 MG PROTEIN/ML IN 50 MM NACL, 5% (V/V) GLYCEROL, 50 MM TRIS/HCL PH 8.0 AND OF 30% (W/V) ...Details: CRYSTALS WERE OBTAINED USING VAPOR-DIFFUSION SITTING-DROP AT 20 DEGREES C BY MIXING EQUAL VOLUMES OF 10 MG PROTEIN/ML IN 50 MM NACL, 5% (V/V) GLYCEROL, 50 MM TRIS/HCL PH 8.0 AND OF 30% (W/V) PEG 1500 IN 100 MM NA/HEPES PH 7.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→54 Å / Num. obs: 94192 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BBY

4bby


Resolution: 2.4→54.17 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.868 / SU B: 22.968 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26972 1033 1.1 %RANDOM
Rwork0.2109 ---
obs0.21152 93155 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0.24 Å2-0.01 Å2
2--0.5 Å2-0.1 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→54.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17446 0 248 161 17855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02218112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.96724523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37752197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08224.047845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.065153083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.19715112
X-RAY DIFFRACTIONr_chiral_restr0.110.22634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113722
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_it0.641.510919
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26217606
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96337193
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1784.56916
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3270 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.340.05
2Btight positional0.260.05
3Ctight positional0.220.05
4Dtight positional0.230.05
1Atight thermal0.290.5
2Btight thermal0.290.5
3Ctight thermal0.350.5
4Dtight thermal0.290.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 77 -
Rwork0.327 6927 -
obs--95.14 %
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)
10.5493-0.14940.08920.30860.00260.5951-0.02930.14820.0788-0.02960.0149-0.0026-0.08520.05810.01440.0207-0.0123-0.01020.18430.02470.087939.0161.35235.59
20.52780.0915-0.22320.34660.00990.8013-0.1027-0.1155-0.02890.0680.0660.00790.19170.1110.03670.06960.05680.00520.14490.01450.079942.43840.69370.611
30.6039-0.3185-0.14380.60740.36090.74490.0378-0.00640.0012-0.03070.0236-0.0307-0.0163-0.0546-0.06150.0123-0.02820.00160.0958-0.02390.08229.19687.246-16.09
40.3030.1038-0.02290.93570.7681.19540.0604-0.13140.13560.07580.05-0.0518-0.0537-0.0605-0.11040.03480.00340.01510.1758-0.0870.157525.556113.02915.988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A81 - 999
2X-RAY DIFFRACTION2B81 - 999
3X-RAY DIFFRACTION3C81 - 999
4X-RAY DIFFRACTION4D81 - 999

+
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