[English] 日本語
Yorodumi
- PDB-7pe4: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pe4
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with UDP-glucose
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP-glucose / thermostable / GTA-fold
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / glycosyltransferase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / 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
BICARBONATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSilva, A. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BTM-TEC/29221/2017 (POCI-01-0145-FEDER-029221). Portugal
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with UDP-glucose
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Feb 7, 2024Group: 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
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0319
Polymers35,1511
Non-polymers8808
Water5,495305
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,06218
Polymers70,3022
Non-polymers1,76016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area8850 Å2
ΔGint-122 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.887, 101.887, 122.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-760-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Glucosyl-3-phosphoglycerate synthase


Mass: 35151.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal sequence KLAAALEHHHHHH corresponds to the linker and hexahistidine tag used for protein purification.
Source: (gene. exp.) Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: gpgS, C731_3243, MHAS_02845 / Production host: Escherichia coli (E. coli)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase

-
Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5; 3 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96112 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013 / Details: 0.96112
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 38917 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.73 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 14.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3768 / Rrim(I) all: 1.052 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P8G

7p8g


Resolution: 2.05→46.58 Å / SU ML: 0.2325 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.192 1950 5.02 %
Rwork0.1602 36928 -
obs0.1618 38878 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.13 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 52 306 2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642477
X-RAY DIFFRACTIONf_angle_d0.80843395
X-RAY DIFFRACTIONf_chiral_restr0.0512409
X-RAY DIFFRACTIONf_plane_restr0.0107440
X-RAY DIFFRACTIONf_dihedral_angle_d12.3845926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.3031460.27732595X-RAY DIFFRACTION99.38
2.1-2.160.2871290.25022593X-RAY DIFFRACTION99.45
2.16-2.220.26141290.22742630X-RAY DIFFRACTION99.78
2.22-2.290.23391440.20322632X-RAY DIFFRACTION99.61
2.29-2.380.24791390.1952648X-RAY DIFFRACTION99.93
2.38-2.470.27721340.18852637X-RAY DIFFRACTION99.89
2.47-2.580.21581620.18742594X-RAY DIFFRACTION99.71
2.58-2.720.221350.18042648X-RAY DIFFRACTION99.89
2.72-2.890.23081360.17972646X-RAY DIFFRACTION99.86
2.89-3.110.20321410.17722646X-RAY DIFFRACTION99.96
3.11-3.430.1861410.1472639X-RAY DIFFRACTION99.93
3.43-3.920.13771470.12172673X-RAY DIFFRACTION99.96
3.92-4.940.14561250.11532668X-RAY DIFFRACTION99.96
4.94-46.580.1731420.15822679X-RAY DIFFRACTION99.75
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)
10.921259226957-0.2233255178830.3343627299552.0828481258-0.4932910631482.217271119920.0886143656823-0.0691307499996-0.195772091879-0.1403060808360.0704226611130.2739815093210.33992580703-0.330610790703-0.1221369281660.334072230266-0.126038668581-0.01096741065680.306782493890.05967861796920.3033845045981.45426991151-25.1545693764.25259797548
25.20638638297-0.082613812203-2.497831965221.75701657026-0.05496568170685.464298147710.071368486418-0.0917896371988-0.02326914569630.00722450405939-0.0175488402581-0.1207779477880.1880587596940.123488741203-0.06277344419180.305139721282-0.00108940490018-0.02586175446310.1733423107310.05759761188140.2565554951513.4713153831-24.09578689670.414034501744
36.081036178731.216619708840.5227518197368.890621381530.8691872531066.123387794390.09313701089220.0477858077218-0.294512427226-0.3170084091230.2038956340620.7656826110970.143073449202-0.673935827686-0.1899345894270.301391819629-0.122508039829-0.03885645549760.3475091959580.1278848486110.363237275369-5.00377798185-26.34410471731.65713295671
44.13341950511-0.177951634443-0.09982086164336.124196520921.577987746620.5544341585650.0111843288752-0.99684162054-0.3504442690180.738388255955-0.0983598440210.2312685271810.590950447749-0.366382415510.09037809632310.349958845197-0.004467926079820.07284515155550.4961665600930.08774901933450.386056388315-4.26736491756-6.095943318532.22563611285
52.97720581572-1.95901559790.8525859578063.14382696287-0.1804714041232.847530245950.128538635942-0.110133661975-0.0667969312446-0.15781853401-0.05082981250520.1826132660990.28479565991-0.214277233037-0.0765270479610.30282123253-0.0678535385050.006595424236320.3336359616810.04975516016890.3186600444970.911233755755-17.526864672-6.38223103895
63.983954577372.35671709658-2.170231634575.46677680289-2.074265090491.343262031690.286740511727-0.6706125710570.2722863289370.911366000306-0.4829921083440.174822707548-0.2550186774110.3798527126890.2354746121630.375538629143-0.0861514421268-0.04019623880070.4879893337690.100493059440.373143688515-2.42019331056-15.63953179336.95883024197
75.962271122861.187518571650.4117106918096.01347332202-1.036525455665.26065651466-0.0254715063881-0.569637000460.09489172434770.1059633449-0.0559047279899-0.335039397364-0.200441600128-0.04077707285620.0756038636040.1913346966060.04814676606110.02588894140960.3282414075950.00500143997690.3355324003218.20495778612-1.06515299052-3.40274076974
83.198624129320.09876158044990.2092282136593.489892389562.286498191555.983298430750.0725929692824-0.3577418297850.1238301976570.0383704691288-0.0470449429203-0.5500763984750.0968648238490.0624917625224-0.07950320648140.1897535078660.016297214540.03790381052790.3795514316160.02906969759380.2924007060616.0112252124-11.573156463-7.09476063275
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 93 )2 - 931 - 92
22chain 'A' and (resid 94 through 140 )94 - 14093 - 139
33chain 'A' and (resid 141 through 163 )141 - 163140 - 162
44chain 'A' and (resid 164 through 192 )164 - 192163 - 181
55chain 'A' and (resid 193 through 237 )193 - 237182 - 226
66chain 'A' and (resid 238 through 256 )238 - 256227 - 245
77chain 'A' and (resid 257 through 289 )257 - 289246 - 278
88chain 'A' and (resid 290 through 321 )290 - 321279 - 310

+
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