[English] 日本語
Yorodumi
- PDB-5i1f: Crystal structure of UTP-glucose-1-phosphate uridylyltransferase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i1f
TitleCrystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia vietnamiensis in complex with Uridine-5'-diphosphate-glucose
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UTP-glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDP-glucose / uridylyltransferase / pyrophosphorylase / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / biosynthetic process
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia vietnamiensis in complex with Uridine-5'-diphosphate-glucose
Authors: Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,35810
Polymers33,5311
Non-polymers8289
Water3,171176
1
A: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

A: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,71720
Polymers67,0612
Non-polymers1,65518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area9190 Å2
ΔGint-212 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.900, 84.900, 252.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-62-

ARG

21A-539-

HOH

-
Components

#1: Protein UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase


Mass: 33530.625 Da / Num. of mol.: 1 / Fragment: BuviA.00118.e.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_6508 / Plasmid: BuviA.00118.e.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4JT02, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MCSG1 screen A4: 2500mM NaCl, 200mM MgCl2, 100mM Tris base/HCl pH 7.0; BuviA.00118.e.B1.PS02498 at 27.5mg/ml + 4mM Glucose-1-phosphate + 4mM UTP + 4mM MgCl2; ; tray: 267283a4, puck sbq8-1, cryo: 20% EG
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 10, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 30405 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 33.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.87
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.15-2.217.30.5423.561100
2.21-2.270.4074.661100
2.27-2.330.3455.431100
2.33-2.40.2936.261100
2.4-2.480.2497.251100
2.48-2.570.2168.41100
2.57-2.670.17510.161100
2.67-2.780.15411.151100
2.78-2.90.13412.581100
2.9-3.040.11614.281100
3.04-3.210.116.381100
3.21-3.40.08718.51199.9
3.4-3.630.07520.42199.9
3.63-3.930.0721.31199.9
3.93-4.30.06622.84199.9
4.3-4.810.06323.691100
4.81-5.550.05623.671100
5.55-6.80.05123.391100
6.8-9.620.04524.18199.6
9.62-500.03923.42193.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.15 Å41.86 Å
Translation2.15 Å41.86 Å

-
Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ux8, chain A

2ux8


Resolution: 2.15→50 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.19
RfactorNum. reflection% reflection
Rfree0.2025 1968 6.49 %
Rwork0.172 --
obs0.1741 30327 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.68 Å2 / Biso mean: 45.623 Å2 / Biso min: 19.36 Å2
Refinement stepCycle: final / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 44 176 2453
Biso mean--31.41 47.23 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072361
X-RAY DIFFRACTIONf_angle_d0.8893215
X-RAY DIFFRACTIONf_chiral_restr0.057365
X-RAY DIFFRACTIONf_plane_restr0.006421
X-RAY DIFFRACTIONf_dihedral_angle_d17.111445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20380.24381190.20861999X-RAY DIFFRACTION100
2.2038-2.26340.23211280.18861968X-RAY DIFFRACTION100
2.2634-2.330.21211350.17831984X-RAY DIFFRACTION100
2.33-2.40520.22371360.18061980X-RAY DIFFRACTION100
2.4052-2.49110.18991440.18162004X-RAY DIFFRACTION100
2.4911-2.59090.24671200.18241987X-RAY DIFFRACTION100
2.5909-2.70870.21121440.18471984X-RAY DIFFRACTION100
2.7087-2.85150.21431490.19231996X-RAY DIFFRACTION100
2.8515-3.03010.22121320.19782037X-RAY DIFFRACTION100
3.0301-3.2640.21991500.18832012X-RAY DIFFRACTION100
3.264-3.59230.19541560.17122005X-RAY DIFFRACTION100
3.5923-4.11170.17541510.14792056X-RAY DIFFRACTION100
4.1117-5.17880.17221530.13762080X-RAY DIFFRACTION100
5.1788-500.21571510.182267X-RAY DIFFRACTION99
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)
12.4063-0.0680.65152.0870.60633.2611-0.0576-0.18220.1530.0880.1752-0.0345-0.5658-0.0565-0.09320.43450.08190.02930.1378-0.02930.218141.338115.45138.3296
24.40011.0375-0.83952.191-0.51192.3814-0.22630.3627-0.2051-0.19910.1033-0.14760.15080.34640.17450.40170.06820.0060.2151-0.02030.226450.42297.1641133.1889
32.6566-0.3145-1.51761.18210.02832.2426-0.0933-0.2021-0.04640.20660.13640.0379-0.24380.2571-0.01090.37950.0706-0.04160.1894-0.01420.209743.245310.6073143.3267
42.2846-1.5112-0.85822.26150.27130.96610.0062-0.36460.5910.24190.1339-0.0234-0.91050.0835-0.02660.83150.30710.08160.2299-0.08080.378631.87926.212154.0692
54.4517-0.9941-0.17824.74050.69181.2907-0.0839-0.2512-0.22520.25390.10760.6712-0.3338-0.41670.01020.51030.19590.05710.30420.02660.329928.61214.4385154.4332
60.4794-0.3045-0.34561.26410.68010.83260.13-0.14210.28130.19570.1672-0.0796-0.48370.11470.05061.07930.09560.05820.023-0.07190.400240.678929.0812136.0169
73.97092.20351.88396.1340.39973.34380.4928-0.41650.39010.2324-0.08260.2914-0.64110.2303-0.21131.2787-0.38090.14310.3616-0.15350.706849.604536.9311125.0489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 47 )A0 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 83 )A48 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 141 )A84 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 206 )A142 - 206
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 248 )A207 - 248
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 271 )A249 - 271
7X-RAY DIFFRACTION7chain 'A' and (resid 272 through 289 )A272 - 289

+
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