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- PDB-4bc7: MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: Arg419His mutant -

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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

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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)295,38612
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

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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

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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: 2.23 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.

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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

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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

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