[English] 日本語
Yorodumi
- PDB-4n69: Soybean Serine Acetyltransferase Complexed with Serine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n69
TitleSoybean Serine Acetyltransferase Complexed with Serine
ComponentsSerine Acetyltransferase Apoenzyme
KeywordsTRANSFERASE / acetyltransferase
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytosol
Similarity search - Function
serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site ...serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / SERINE / serine O-acetyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYi, H. / Dey, S. / Kumaran, S. / Krishnan, H.B. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of soybean serine acetyltransferase and formation of the cysteine regulatory complex as a molecular chaperone.
Authors: Yi, H. / Dey, S. / Kumaran, S. / Lee, S.G. / Krishnan, H.B. / Jez, J.M.
History
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Serine Acetyltransferase Apoenzyme
B: Serine Acetyltransferase Apoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2036
Polymers60,8032
Non-polymers4004
Water8,377465
1
A: Serine Acetyltransferase Apoenzyme
hetero molecules

A: Serine Acetyltransferase Apoenzyme
hetero molecules

A: Serine Acetyltransferase Apoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8059
Polymers91,2053
Non-polymers6006
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7090 Å2
ΔGint-64 kcal/mol
Surface area26330 Å2
MethodPISA
2
B: Serine Acetyltransferase Apoenzyme
hetero molecules

B: Serine Acetyltransferase Apoenzyme
hetero molecules

B: Serine Acetyltransferase Apoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8059
Polymers91,2053
Non-polymers6006
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7000 Å2
ΔGint-61 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.368, 111.368, 143.456
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-302-

PO4

21A-302-

PO4

31B-502-

PO4

41B-502-

PO4

-
Components

#1: Protein Serine Acetyltransferase Apoenzyme


Mass: 30401.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Production host: Escherichia coli (E. coli) / References: UniProt: I1KHY6, serine O-acetyltransferase
#2: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DISCREPANCIES ARE ARISING FROM THE DIFFERENT UNPROT SEQUENCE AND THE SPECIFIC CLONE USED FOR ...THE DISCREPANCIES ARE ARISING FROM THE DIFFERENT UNPROT SEQUENCE AND THE SPECIFIC CLONE USED FOR STRUCTURAL STUDIES

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.32 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→32.15 Å / Num. all: 59887 / Num. obs: 57084 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.149 Å / SU ML: 0.17 / σ(F): 1.96 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 3030 5.06 %
Rwork0.1671 --
obs0.1685 54204 97.37 %
all-61256 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→32.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 24 465 4117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063800
X-RAY DIFFRACTIONf_angle_d0.9875184
X-RAY DIFFRACTIONf_dihedral_angle_d11.9111354
X-RAY DIFFRACTIONf_chiral_restr0.04604
X-RAY DIFFRACTIONf_plane_restr0.005670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7998-1.82790.26381530.24022636X-RAY DIFFRACTION99
1.8279-1.85790.25631420.22892633X-RAY DIFFRACTION99
1.8579-1.88990.26641300.21832592X-RAY DIFFRACTION99
1.8899-1.92420.27051360.21542652X-RAY DIFFRACTION99
1.9242-1.96130.24231510.20092607X-RAY DIFFRACTION99
1.9613-2.00130.2251280.19692635X-RAY DIFFRACTION99
2.0013-2.04480.21111390.17712613X-RAY DIFFRACTION99
2.0448-2.09230.1941450.17522640X-RAY DIFFRACTION99
2.0923-2.14470.21271300.17672630X-RAY DIFFRACTION99
2.1447-2.20260.20531280.17362600X-RAY DIFFRACTION99
2.2026-2.26740.18811400.16542631X-RAY DIFFRACTION99
2.2674-2.34060.19021450.16922591X-RAY DIFFRACTION98
2.3406-2.42420.211270.16422659X-RAY DIFFRACTION98
2.4242-2.52120.23221400.16542584X-RAY DIFFRACTION98
2.5212-2.63590.17731500.17082579X-RAY DIFFRACTION98
2.6359-2.77480.19621330.16682569X-RAY DIFFRACTION97
2.7748-2.94860.17941430.16352593X-RAY DIFFRACTION97
2.9486-3.17610.18681530.16822541X-RAY DIFFRACTION97
3.1761-3.49530.19341460.15532569X-RAY DIFFRACTION96
3.4953-4.00030.16941230.14022521X-RAY DIFFRACTION95
4.0003-5.03680.16091270.13752508X-RAY DIFFRACTION94
5.0368-32.15430.22061210.19832274X-RAY DIFFRACTION86
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)
11.2598-0.3775-0.01342.77570.94482.3101-0.06930.2251-0.1578-0.07860.1107-0.43260.2280.4559-0.13890.19350.05130.03620.3332-0.06330.2829-31.980522.101815.5117
22.51980.0841-0.20812.39320.74483.4419-0.12070.1225-0.2149-0.05530.096-0.11680.4342-0.0377-0.00190.18480.01160.01160.1482-0.01390.1804-48.048416.604316.6284
32.85961.4126-1.14884.6582-2.26545.5909-0.22930.2372-0.4677-0.49880.0767-0.52560.29760.3915-0.03890.38380.04690.08750.3392-0.08870.3128-37.788713.91812.0606
43.0285-0.009-0.71840.63690.62763.1707-0.08910.2229-0.1736-0.24160.0543-0.11790.0390.0942-0.02090.3092-0.01380.020.2405-0.02070.1859-49.581318.15894.1742
54.2985-0.8563-0.9152.4789-1.15072.56630.11220.7966-0.0343-0.1408-0.02420.23160.2313-0.4485-0.09390.3130.02380.02440.4305-0.07630.2729-53.980118.2421-9.2362
65.6024-1.0398-0.59483.445-0.7243.41330.28771.2169-0.0861-0.61130.00520.12030.7643-0.4454-0.04860.52120.0974-0.03890.7324-0.02230.2786-51.754517.5677-17.9507
72.1716-1.2675-1.76665.36630.97733.88140.51681.43720.2382-0.5799-0.4155-0.13240.1947-0.1828-0.09440.70310.22580.06281.06830.0480.3518-48.810520.0646-23.5344
85.00821.1786-1.20291.597-0.40641.89680.10970.07740.40590.4880.07860.3364-0.5186-0.6042-0.17250.35460.12630.11370.3675-0.01150.3378-24.098417.044-12.4075
91.20890.3637-0.19262.3149-0.03822.23860.0372-0.00580.04330.1111-0.0250.24670.04-0.2809-0.02040.13170.01510.02370.1980.00110.1807-16.88693.8622-18.0346
102.79891.29671.28774.08881.75025.02940.1647-0.32880.26490.4668-0.34270.5393-0.1468-0.5407-0.01650.3035-0.00440.12430.4184-0.03690.2858-24.74866.3813-2.3759
111.5726-0.6404-0.50764.54180.23292.71730.0741-0.1304-0.02310.4082-0.12870.2178-0.0615-0.1524-0.02540.2651-0.02550.03090.27070.00460.1569-15.1447-1.5757-6.6151
123.4444-1.41870.47843.71391.64953.1667-0.2804-0.2827-0.11470.35690.3415-0.06180.38160.0982-0.07960.32940.01380.08320.34090.00020.2463-13.6297-4.45776.5667
133.1471-0.5484-0.48243.51041.293.0189-0.199-1.25690.00211.10150.4833-0.10350.7293-0.3238-0.0540.66420.2044-0.00340.8162-0.00270.3038-14.3504-2.334120.0815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 13:51 )A13 - 51
2X-RAY DIFFRACTION2( CHAIN A AND RESID 52:85 )A52 - 85
3X-RAY DIFFRACTION3( CHAIN A AND RESID 86:102 )A86 - 102
4X-RAY DIFFRACTION4( CHAIN A AND RESID 103:170 )A103 - 170
5X-RAY DIFFRACTION5( CHAIN A AND RESID 171:220 )A171 - 220
6X-RAY DIFFRACTION6( CHAIN A AND RESID 221:240 )A221 - 240
7X-RAY DIFFRACTION7( CHAIN A AND RESID 241:255 )A241 - 255
8X-RAY DIFFRACTION8( CHAIN B AND RESID 13:34 )B13 - 34
9X-RAY DIFFRACTION9( CHAIN B AND RESID 35:85 )B35 - 85
10X-RAY DIFFRACTION10( CHAIN B AND RESID 86:102 )B86 - 102
11X-RAY DIFFRACTION11( CHAIN B AND RESID 103:151 )B103 - 151
12X-RAY DIFFRACTION12( CHAIN B AND RESID 152:220 )B152 - 220
13X-RAY DIFFRACTION13( CHAIN B AND RESID 221:255 )B221 - 255

+
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