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- PDB-4bc9: MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: WILD-TYPE, ADD... -

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Basic information

Entry
Database: PDB / ID: 4bc9
TitleMAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: WILD-TYPE, ADDUCT WITH CYANOETHYL
ComponentsALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMALAlkylglycerone phosphate synthase
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
propanenitrile / FLAVIN-ADENINE DINUCLEOTIDE / Alkyldihydroxyacetonephosphate synthase, peroxisomal
Similarity search - Component
Biological speciesCAVIA PORCELLUS (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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_conn / 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_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)295,40515
Polymers291,7554
Non-polymers3,65111
Water5,765320
1
C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6557
Polymers145,8772
Non-polymers1,7775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-65.9 kcal/mol
Surface area38090 Å2
MethodPISA
2
A: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7518
Polymers145,8772
Non-polymers1,8736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-72.5 kcal/mol
Surface area38940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.910, 98.620, 106.280
Angle α, β, γ (deg.)90.92, 89.84, 95.66
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

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYS1AA81 - 10281 - 102
21GLYGLYLYSLYS1BB81 - 10281 - 102
31GLYGLYLYSLYS1CC81 - 10281 - 102
41GLYGLYLYSLYS1DD81 - 10281 - 102
12SERSERARGARG4AA158 - 265158 - 265
22SERSERARGARG4BB158 - 265158 - 265
32SERSERARGARG4CC158 - 265158 - 265
42SERSERARGARG4DD158 - 265158 - 265
13VALVALGLNGLN4AA278 - 425278 - 425
23VALVALGLNGLN4BB278 - 425278 - 425
33VALVALGLNGLN4CC278 - 425278 - 425
43VALVALGLNGLN4DD278 - 425278 - 425
14VALVALGLYGLY4AA465 - 472465 - 472
24VALVALGLYGLY4BB465 - 472465 - 472
34VALVALGLYGLY4CC465 - 472465 - 472
44VALVALGLYGLY4DD465 - 472465 - 472
15METMETTYRTYR4AA514 - 578514 - 578
25METMETTYRTYR4BB514 - 578514 - 578
35METMETTYRTYR4CC514 - 578514 - 578
45METMETTYRTYR4DD514 - 578514 - 578
16VALVALLEULEU4AA594 - 658594 - 658
26VALVALLEULEU4BB594 - 658594 - 658
36VALVALLEULEU4CC594 - 658594 - 658
46VALVALLEULEU4DD594 - 658594 - 658

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.97133, 0.224622, -0.077864), (0.224965, -0.974357, -0.004451), (-0.076867, -0.013193, -0.996954)-6.14117, 90.33826, 109.0787
3given(0.985702, 0.02544, 0.166564), (0.143678, 0.389484, -0.909758), (-0.088018, 0.920682, 0.38026)14.1398, 8.37867, -36.77331
4given(0.995264, 0.046522, -0.085358), (0.096625, -0.377042, 0.921142), (0.01067, -0.925027, -0.379752)11.98444, 85.4635, 144.05267

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Components

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


Mass: 72938.695 Da / Num. of mol.: 4
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-CNV / propanenitrile / Propionitrile


Mass: 55.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


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


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCYANOETHYL (CNV): CYANOETHYL COVALENT ADDUCT WITH THE FLAVIN N5 ATOM

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.18 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) PEG1500 IN 100 MM NA/HEPES PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / 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: 92832 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.7.0027refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BBY

4bby


Resolution: 2.41→54.06 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.888 / SU B: 9.211 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24767 1014 1.1 %RANDOM
Rwork0.18627 ---
obs0.18695 91818 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.209 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0.11 Å2-0.62 Å2
2---1.51 Å20.55 Å2
3---3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.41→54.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17260 0 243 320 17823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217923
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.651.96924279
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63352193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4823.988820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.561153015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.07715112
X-RAY DIFFRACTIONr_chiral_restr0.1050.22629
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113574
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
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3052medium positional0.420.5
2B3052medium positional0.350.5
3C3052medium positional0.330.5
4D3052medium positional0.350.5
1A186tight thermal3.240.5
2B186tight thermal4.820.5
3C186tight thermal5.340.5
4D186tight thermal4.530.5
1A3052medium thermal3.772
2B3052medium thermal3.82
3C3052medium thermal42
4D3052medium thermal4.72
LS refinement shellResolution: 2.41→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 69 -
Rwork0.247 6675 -
obs--96.74 %

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