[English] 日本語
Yorodumi
- PDB-3ogz: Protein structure of USP from L. major in Apo-form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ogz
TitleProtein structure of USP from L. major in Apo-form
ComponentsUDP-sugar pyrophosphorylase
KeywordsTRANSFERASE / left handed beta helix / Rossmann Fold / UDP sugar pyrophosphorylase
Function / homology
Function and homology information


UTP-monosaccharide-1-phosphate uridylyltransferase / uridylyltransferase activity
Similarity search - Function
UDP N-Acetylglucosamine Acyltransferase; domain 1 - #30 / UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex ...UDP N-Acetylglucosamine Acyltransferase; domain 1 - #30 / UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
UTP-monosaccharide-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.03 Å
AuthorsDickmanns, A. / Damerow, S. / Neumann, P. / Schulz, E.-C. / Lamerz, A. / Routier, F. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural basis for the broad substrate range of the UDP-sugar pyrophosphorylase from Leishmania major.
Authors: Dickmanns, A. / Damerow, S. / Neumann, P. / Schulz, E.C. / Lamerz, A.C. / Routier, F.H. / Ficner, R.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: UDP-sugar pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1152
Polymers69,0231
Non-polymers921
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.392, 123.196, 61.342
Angle α, β, γ (deg.)90.000, 104.320, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

21A-775-

HOH

31A-873-

HOH

41A-1016-

HOH

-
Components

#1: Protein UDP-sugar pyrophosphorylase


Mass: 69023.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: 5ASKH / Gene: USP / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D3G6S4, UTP-monosaccharide-1-phosphate uridylyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1-0.2 M sodium tartrate, 16-20% PEG5000, 10 mM DTT, pH 7-8, vapor diffusion, sitting drop, temperature 292K
PH range: 7-8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE, / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 28.07 / Number: 151692 / Rmerge(I) obs: 0.041 / Χ2: 1 / D res high: 2.18 Å / D res low: 50 Å / Num. obs: 39732 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.75098.510.0231.0123.7
3.734.710010.031.0983.8
3.263.7399.910.0311.013.8
2.963.2610010.0451.0113.9
2.752.9610010.0720.9983.9
2.582.7510010.1230.9793.9
2.462.5810010.1721.0013.9
2.352.4610010.2640.9653.8
2.262.3510010.620.9823.8
2.182.2699.810.3220.9843.7
ReflectionResolution: 2.03→50 Å / Num. all: 49970 / Num. obs: 49970 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 35.03 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Χ2: 0.989 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.03-2.14.40.50849860.917100
2.1-2.194.40.43349930.987100
2.19-2.294.40.24550020.989100
2.29-2.414.40.23249840.98100
2.41-2.564.50.12150340.995100
2.56-2.764.50.08449691.004100
2.76-3.034.50.05350271.004100
3.03-3.474.50.03549940.993100
3.47-4.374.40.02750351.01100
4.37-504.30.02249461.01397.3

-
Phasing

PhasingMethod: SIRAS

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHARPphasing
RESOLVEphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
DENZOdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.03→29.741 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2511 5.06 %RANDOM
Rwork0.1843 ---
obs0.1861 49601 98.86 %-
all-49970 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.224 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 163.72 Å2 / Biso mean: 48.5881 Å2 / Biso min: 21.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.8092 Å2-0 Å20.167 Å2
2---7.4496 Å20 Å2
3---4.6404 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.276 Å
Luzzati d res low-8 Å
Luzzati sigma a0.26 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.03→29.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 6 397 4897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054654
X-RAY DIFFRACTIONf_angle_d0.8436328
X-RAY DIFFRACTIONf_chiral_restr0.058721
X-RAY DIFFRACTIONf_plane_restr0.003825
X-RAY DIFFRACTIONf_dihedral_angle_d12.2881712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.06410.26481240.21832564268897
2.0641-2.10630.23541370.209726532790100
2.1063-2.15210.24891370.211426452782100
2.1521-2.20210.33011440.2712567271198
2.2021-2.25720.41621330.37742563269697
2.2572-2.31820.3571530.33712400255393
2.3182-2.38630.23791460.208526602806100
2.3863-2.46330.20441600.180226142774100
2.4633-2.55130.24191350.173126652800100
2.5513-2.65340.23221320.182526072739100
2.6534-2.77410.21391420.179826432785100
2.7741-2.92020.19511460.180226762822100
2.9202-3.1030.20431420.171226182760100
3.103-3.34230.20781370.168726402777100
3.3423-3.67810.18981350.15526702805100
3.6781-4.20910.18651370.14526402777100
4.2091-5.29810.17031410.136126712812100
5.2981-29.74390.19291300.16992594272496
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)
10.85010.2846-0.14410.79280.13140.54950.1801-0.14870.21920.2031-0.16330.27180.2284-0.00590.00960.4559-0.18280.13370.4027-0.10090.55588.348230.002948.7892
22.06461.46440.98631.23570.79492.0085-0.59690.15731.0189-0.79670.1961-0.3214-1.30130.33810.2990.6964-0.21160.00630.38820.03121.042831.317512.957323.8109
31.2859-0.19470.0751.61250.40361.27110.1263-0.033-0.01320.0147-0.1269-0.2357-0.02680.0314-0.00570.2908-0.02520.00140.28910.03250.266910.0695-6.665224.6897
40.85330.0893-0.17270.19950.3890.980.0710.24820.1588-0.38820.08560.09-0.32790.0138-0.13310.6295-0.0742-0.04680.4126-0.01350.533215.19226.494930.1611
51.3469-0.02580.43130.92440.89821.13080.17390.03380.2726-0.2552-0.28160.2374-0.1217-0.25160.12160.3966-0.0872-0.0210.3638-0.09710.5686.156926.072638.2521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 1:76)A1 - 76
2X-RAY DIFFRACTION2chain A and (resid 77:85 or resid 300:356)A77 - 85
3X-RAY DIFFRACTION2chain A and (resid 77:85 or resid 300:356)A300 - 356
4X-RAY DIFFRACTION3chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A86 - 195
5X-RAY DIFFRACTION3chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A224 - 299
6X-RAY DIFFRACTION3chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A357 - 378
7X-RAY DIFFRACTION3chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A406 - 615
8X-RAY DIFFRACTION4chain A and (resid 379:405)A379 - 405
9X-RAY DIFFRACTION5chain A and (resid 196:223)A196 - 223

+
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