[English] 日本語
Yorodumi
- PDB-4j8l: CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j8l
TitleCRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT protein YhfS from Escherichia coli
ComponentsUncharacterized protein YhfS
KeywordsUNKNOWN FUNCTION / Two domains / PLP covalently attached to Lysine
Function / homology
Function and homology information


O-acetylhomoserine aminocarboxypropyltransferase activity / L-homocysteine biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #130 / YhfS-like, C-terminal domain / O-acetylhomoserine/O-acetylserine sulfhydrylase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Aspartate Aminotransferase, domain 1 - #130 / YhfS-like, C-terminal domain / O-acetylhomoserine/O-acetylserine sulfhydrylase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Uncharacterized protein YhfS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.651 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Xiang, D.F. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the pyridoxal-5'-phosphate dependent protein yhfs from escherichia coli
Authors: Fedorov, A.A. / Fedorov, E.V. / Xiang, D.F. / Raushel, F.M. / Almo, S.C.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein YhfS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3986
Polymers39,0531
Non-polymers3455
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein YhfS
hetero molecules

A: Uncharacterized protein YhfS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,79612
Polymers78,1062
Non-polymers69010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area4680 Å2
ΔGint-43 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.915, 134.915, 75.142
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21A-752-

HOH

31A-756-

HOH

41A-758-

HOH

-
Components

#1: Protein Uncharacterized protein YhfS


Mass: 39052.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yhfS, b3376, JW3339 / Production host: Escherichia coli (E. coli) / References: UniProt: P45545
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4M sodium acetate, 0.1M sodium cacodylate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.651→46.121 Å / Num. all: 48578 / Num. obs: 48578 / % possible obs: 99.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.651→46.121 Å / SU ML: 0.16 / σ(F): 1 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 2454 5.05 %RANDOM
Rwork0.1691 ---
obs0.1705 48578 99.78 %-
all-48578 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.651→46.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 20 276 3028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062820
X-RAY DIFFRACTIONf_angle_d1.0683836
X-RAY DIFFRACTIONf_dihedral_angle_d13.0621043
X-RAY DIFFRACTIONf_chiral_restr0.069447
X-RAY DIFFRACTIONf_plane_restr0.006510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6514-1.68320.2861150.22722499X-RAY DIFFRACTION98
1.6832-1.71750.23121320.20612512X-RAY DIFFRACTION100
1.7175-1.75490.2351240.19052542X-RAY DIFFRACTION100
1.7549-1.79570.24611500.19952506X-RAY DIFFRACTION100
1.7957-1.84060.23621170.18592543X-RAY DIFFRACTION100
1.8406-1.89040.21711380.17672518X-RAY DIFFRACTION100
1.8904-1.9460.23781470.17112518X-RAY DIFFRACTION100
1.946-2.00880.20431500.17322520X-RAY DIFFRACTION100
2.0088-2.08060.20051410.16432547X-RAY DIFFRACTION100
2.0806-2.16390.21211190.16772549X-RAY DIFFRACTION100
2.1639-2.26240.20791260.172552X-RAY DIFFRACTION100
2.2624-2.38170.21381370.16942559X-RAY DIFFRACTION100
2.3817-2.53090.21711320.17472581X-RAY DIFFRACTION100
2.5309-2.72630.17531350.17932569X-RAY DIFFRACTION100
2.7263-3.00060.21081450.18542586X-RAY DIFFRACTION100
3.0006-3.43460.19581580.17762589X-RAY DIFFRACTION100
3.4346-4.32680.15651470.14762630X-RAY DIFFRACTION100
4.3268-46.1390.17971410.15522804X-RAY DIFFRACTION100
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)
12.1218-2.1999-1.82427.43312.88573.44470.07380.2711-0.174-0.6479-0.15270.1524-0.1035-0.05760.05390.1583-0.019-0.04480.1657-0.00650.136525.280551.202536.403
20.69511.3472-1.90822.7456-4.00025.89130.0996-0.07740.15460.1865-0.0140.24-0.2493-0.0003-0.10490.1344-0.00290.02930.1635-0.00710.199215.830861.423760.3316
32.38120.99232.17020.9730.10287.4730.0266-0.04850.0975-0.0938-0.0150.2989-0.3415-0.24480.00220.09020.01280.01650.11420.01030.168914.674253.132552.2987
41.1066-0.4885-0.1441.7535-0.07041.7453-0.03910.1658-0.3512-0.21370.00310.140.4001-0.223-0.020.2569-0.0719-0.01550.1719-0.06880.280817.689229.171445.7156
50.7893-0.053-0.45760.97880.23252.01150.02880.069-0.0314-0.05340.02390.1590.103-0.1236-0.05040.1519-0.0089-0.00810.1368-0.00980.208119.333844.957351.3608
64.8586-0.9281-5.31430.85160.94676.31220.11-0.03760.1541-0.18550.08160.0666-0.14080.2009-0.20620.1439-0.0003-0.010.1196-0.01090.122233.463551.814341.7231
72.3673-0.646-0.18281.54250.43732.00010.00140.1916-0.3196-0.1261-0.039-0.12550.11640.0940.01940.19120.02260.06240.1225-0.00790.204147.949435.685537.8333
81.7673-0.2685-0.15954.09741.97142.2116-0.0183-0.0018-0.27690.217-0.04330.03610.3024-0.02540.07770.14510.00830.02360.1324-0.00580.177342.604437.160847.0511
95.05660.7016-1.05584.20270.14011.5383-0.0579-0.03050.0336-0.32610.0499-0.2878-0.03180.10120.00450.21420.01680.04450.1362-0.02350.106949.332444.390339.1797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 73 )
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 170 )
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 261 )
7X-RAY DIFFRACTION7chain 'A' and (resid 262 through 299 )
8X-RAY DIFFRACTION8chain 'A' and (resid 300 through 336 )
9X-RAY DIFFRACTION9chain 'A' and (resid 337 through 361 )

+
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