[English] 日本語
Yorodumi
- PDB-2w8v: SPT with PLP, N100W -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w8v
TitleSPT with PLP, N100W
ComponentsSERINE PALMITOYLTRANSFERASESerine C-palmitoyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


serine C-palmitoyltransferase / sphingolipid metabolic process / biosynthetic process / acyltransferase activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Serine palmitoyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS PAUCIMOBILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsRaman, M.C.C. / Johnson, K.A. / Campopiano, D.J. / Naismith, J.H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The External-Aldimine Form of Serine Palmitoyltranserase; Structural, Kinetic and Spectroscopic Analysis of the Wild-Type Enzyme and Hsan1 Mutant Mimics.
Authors: Raman, M.C.C. / Johnson, K.A. / Yard, B.A. / Lowther, J. / Carter, L.G. / Naismith, J.H. / Campopiano, D.J.
History
DepositionJan 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE PALMITOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3502
Polymers46,1031
Non-polymers2471
Water7,188399
1
A: SERINE PALMITOYLTRANSFERASE
hetero molecules

A: SERINE PALMITOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7004
Polymers92,2052
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8650 Å2
ΔGint-68.3 kcal/mol
Surface area33560 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.920, 109.786, 91.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein SERINE PALMITOYLTRANSFERASE / Serine C-palmitoyltransferase / SPT


Mass: 46102.660 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-420 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PAUCIMOBILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q93UV0
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 100 TO TRP
Sequence detailsC-TER HIS TAG NOTE ENGINEERED MUTATION AT N100W NOTE THE MUTATION IS N100W, HOWEVER, WE CAN ONLY SEE ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.43→27 Å / Num. obs: 62574 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 88

-
Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→27.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.277 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. THE C-TERMINUS IS DISORDERED, BUT OXT IS USED TO MODEL LAST ORDERED ATOM LINK WITH 2W8J, 2W8T,2W8U NOTE ALTHOUGH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. THE C-TERMINUS IS DISORDERED, BUT OXT IS USED TO MODEL LAST ORDERED ATOM LINK WITH 2W8J, 2W8T,2W8U NOTE ALTHOUGH N100W IS MUTATION, WE ONLY CAN MODEL AN ALA
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3305 5 %RANDOM
Rwork0.161 ---
obs0.162 62574 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.43→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 15 399 3418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223109
X-RAY DIFFRACTIONr_bond_other_d0.0010.022095
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9724213
X-RAY DIFFRACTIONr_angle_other_deg0.82535114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2345409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87123.492126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68915528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9071521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
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_it0.6831.51981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12623171
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.79931128
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7914.51036
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.77335204
X-RAY DIFFRACTIONr_sphericity_free2.9633399
X-RAY DIFFRACTIONr_sphericity_bonded1.01635141
LS refinement shellResolution: 1.43→1.47 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 195
Rwork0.243 3809
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)
10.86950.2033-0.65610.289-0.58731.28220.0142-0.0717-0.15530.1687-0.0440.0018-0.33560.04950.02970.2855-0.03350.00220.2126-0.00420.16969.407-14.198-2.735
21.0637-0.0784-0.32230.48240.10991.2483-0.01310.0857-0.0463-0.0622-0.0011-0.0617-0.01390.01940.01430.0398-0.01490.01730.0471-0.00790.0985-4.535-30.096-19.512
30.4623-0.1228-0.16821.6397-0.05240.7725-0.0142-0.01020.05480.0783-0.01150.0038-0.1536-0.06330.02560.04180.0185-0.02070.0526-0.01170.0525-16.881-6.582-18.276
40.9621-0.1450.14031.4193-0.04350.7285-0.05430.04620.0336-0.0663-0.0033-0.018-0.0544-0.07410.05750.01360.0028-0.00480.0402-0.01460.0321-12.066-18.656-25.902
51.7350.08690.50211.08480.03292.03190.0123-0.13390.09720.1438-0.0408-0.0468-0.1544-0.02150.02840.0497-0.01380.0150.05460.00260.0448-11.123-20.7654.518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 57
2X-RAY DIFFRACTION2A58 - 114
3X-RAY DIFFRACTION3A115 - 252
4X-RAY DIFFRACTION4A253 - 315
5X-RAY DIFFRACTION4A1265
6X-RAY DIFFRACTION5A316 - 419

+
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