[English] 日本語
Yorodumi
- PDB-7l81: x-ray structure of the psychrobacter cryohalolentis N-acetyltrans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l81
Titlex-ray structure of the psychrobacter cryohalolentis N-acetyltransferase Pcryo_0637 in the presence of coenzyme A and
ComponentsPutative acetyl transferase protein
KeywordsTRANSFERASE / beta helix / N-acetyltransferase / lipopolysaccharide
Function / homology
Function and homology information


transferase activity / nucleotide binding
Similarity search - Function
Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
COENZYME A / Chem-UD4 / Acetyl transferase protein
Similarity search - Component
Biological speciesPsychrobacter cryohalolentis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsLinehan, M.P. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134643 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar.
Authors: Linehan, M.P. / Thoden, J.B. / Holden, H.M.
History
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Putative acetyl transferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6649
Polymers23,6801
Non-polymers1,9848
Water4,432246
1
AAA: Putative acetyl transferase protein
hetero molecules

AAA: Putative acetyl transferase protein
hetero molecules

AAA: Putative acetyl transferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,99327
Polymers71,0413
Non-polymers5,95324
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 area9890 Å2
ΔGint-162 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.050, 97.050, 66.032
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11AAA-303-

CL

21AAA-307-

MPD

31AAA-307-

MPD

41AAA-606-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Putative acetyl transferase protein


Mass: 23680.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5) (bacteria)
Strain: ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5 / Gene: Pcryo_0637 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QD33

-
Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-UD4 / UDP-2-acetamido-4-amino-2,4,6-trideoxy-alpha-D-glucopyranose / (2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl


Mass: 590.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28N4O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
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, hanging drop / pH: 7.5
Details: 23-26 % MPD, 100 mM HEPES. protein incubated with 5 mM coenzyme A and 10 mM UDP-2-acetamido-4-amino-2,4,3-trideoxy-D-glucose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 56136 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rsym value: 0.054 / Net I/σ(I): 20.3
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10804 / Rsym value: 0.448 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7l7y

7l7y


Resolution: 1.3→28.643 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.09 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1945 2857 5.089 %
Rwork0.1731 53279 -
all0.174 --
obs-56136 98.332 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.035 Å20 Å2
2--0.07 Å20 Å2
3----0.228 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 127 246 1985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131810
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171731
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6512488
X-RAY DIFFRACTIONr_angle_other_deg1.4271.5784013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.595233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1423.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50315288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.98155
X-RAY DIFFRACTIONr_chiral_restr0.0730.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02329
X-RAY DIFFRACTIONr_nbd_refined0.2090.2335
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.21635
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2889
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2172
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2490.219
X-RAY DIFFRACTIONr_nbd_other0.2520.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2790.224
X-RAY DIFFRACTIONr_mcbond_it1.4341.318881
X-RAY DIFFRACTIONr_mcbond_other1.3941.314880
X-RAY DIFFRACTIONr_mcangle_it2.011.9711104
X-RAY DIFFRACTIONr_mcangle_other2.0121.9751105
X-RAY DIFFRACTIONr_scbond_it2.5351.691929
X-RAY DIFFRACTIONr_scbond_other2.5341.692930
X-RAY DIFFRACTIONr_scangle_it3.6492.4511375
X-RAY DIFFRACTIONr_scangle_other3.6482.4531376
X-RAY DIFFRACTIONr_lrange_it5.18918.3062042
X-RAY DIFFRACTIONr_lrange_other5.19118.3222043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3330.3971990.4023763X-RAY DIFFRACTION93.7308
1.333-1.370.3822060.3613748X-RAY DIFFRACTION95.669
1.37-1.410.321760.3283574X-RAY DIFFRACTION94.2448
1.41-1.4530.312310.3083530X-RAY DIFFRACTION96.7584
1.453-1.5010.291860.2553530X-RAY DIFFRACTION98.4371
1.501-1.5530.2591950.2243400X-RAY DIFFRACTION99.282
1.553-1.6120.2311640.2033364X-RAY DIFFRACTION99.5766
1.612-1.6780.2061620.183186X-RAY DIFFRACTION99.5836
1.678-1.7520.181860.1673032X-RAY DIFFRACTION99.8449
1.752-1.8380.1841600.1522967X-RAY DIFFRACTION99.9361
1.838-1.9370.1761500.1412809X-RAY DIFFRACTION99.8313
1.937-2.0540.1551440.1412616X-RAY DIFFRACTION99.711
2.054-2.1960.1531150.132491X-RAY DIFFRACTION99.8467
2.196-2.3710.145940.1252378X-RAY DIFFRACTION99.8788
2.371-2.5970.1621320.1232096X-RAY DIFFRACTION99.8655
2.597-2.9030.1391080.1211904X-RAY DIFFRACTION100
2.903-3.350.155930.131742X-RAY DIFFRACTION100
3.35-4.0990.139690.1241425X-RAY DIFFRACTION100
4.099-5.7780.134650.1281106X-RAY DIFFRACTION100
5.778-28.6430.198220.173618X-RAY DIFFRACTION98.7654

+
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