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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pdo
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with UDP
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP / thermostable / GTA-fold
Function / homologyglucosyl-3-phosphoglycerate synthase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Function and homology information
Biological speciesMycolicibacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSilva, A. / Nunes-Costa, D. / 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
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionAug 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 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)35,5596
Polymers35,0131
Non-polymers5465
Water3,297183
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,11812
Polymers70,0262
Non-polymers1,09210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
Buried area6990 Å2
ΔGint-119 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.338, 101.338, 122.532
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

#1: Protein Glucosyl-3-phosphoglycerate synthase /


Mass: 35012.984 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 DSM 44199 (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: gpgS, C731_3243, MHAS_02845 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 298 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 43448 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.16 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Net I/σ(I): 17.1
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4232 / Rpim(I) all: 0.371 / Rrim(I) all: 0.957 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P8G

7p8g


Resolution: 1.97→46.57 Å / SU ML: 0.2412 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1954 2184 5.03 %
Rwork0.1822 41200 -
obs0.1829 43384 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.77 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 29 183 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652355
X-RAY DIFFRACTIONf_angle_d0.85193221
X-RAY DIFFRACTIONf_chiral_restr0.0542389
X-RAY DIFFRACTIONf_plane_restr0.0105413
X-RAY DIFFRACTIONf_dihedral_angle_d12.2467863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.33211520.31442547X-RAY DIFFRACTION98.68
2.01-2.060.24941210.26932540X-RAY DIFFRACTION98.63
2.06-2.110.27141440.24972552X-RAY DIFFRACTION99.19
2.11-2.170.26751340.22752551X-RAY DIFFRACTION98.97
2.17-2.230.26241240.21032578X-RAY DIFFRACTION99.34
2.23-2.30.2481230.20442588X-RAY DIFFRACTION99.09
2.3-2.390.22611440.20452533X-RAY DIFFRACTION99.48
2.39-2.480.25341370.21022586X-RAY DIFFRACTION99.6
2.48-2.590.25561350.2062560X-RAY DIFFRACTION99.48
2.6-2.730.25961150.20892613X-RAY DIFFRACTION99.82
2.73-2.90.24731610.2272567X-RAY DIFFRACTION99.96
2.9-3.130.25331400.22432573X-RAY DIFFRACTION99.63
3.13-3.440.21351310.18792578X-RAY DIFFRACTION99.93
3.44-3.940.15091450.1492594X-RAY DIFFRACTION99.96
3.94-4.960.12481400.12682609X-RAY DIFFRACTION99.96
4.96-46.570.15581380.16512631X-RAY DIFFRACTION99.89
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)
11.422171216470.225516595556-0.1958387364931.73228825872-0.6600605073572.289182908220.07047551864050.09915824287450.127259680750.1579535315750.07967886183550.171553274956-0.383226066272-0.312831022152-0.1420391213620.4189462269330.122400182250.02803753653080.3285058812910.05137733134330.3247277928614.93549667103-25.6785466728-36.4262572306
20.7463680789290.869097690377-0.4661085831272.81383980691-0.9127767134131.876404979810.06520356791430.1590541047370.156920306192-0.0008204959877010.1092426634490.323412626185-0.242009364744-0.431318913619-0.1779355741450.3572347616850.09779254196430.01020348299610.4572501024280.05793245560290.3350425065180.961772960785-30.6525283235-33.023426243
33.161661832870.1381381523551.473349013265.16919145009-2.473083206961.959025851920.2195562997240.5524153108390.117288943494-0.374350679769-0.02696438292870.0008146372113310.1020188810280.0191796128429-0.1647246971650.3380450593930.07710069333530.007585750580.5627162124870.0796903010810.297790374193-0.732102281015-34.70098029-32.6606473696
44.00434451233-0.916513514646-0.7567390027496.658168798622.081246730538.09603896604-0.03281247162810.458163910432-0.204149233323-0.1908754044970.114694635239-0.3458895651450.2568740148120.392371611535-0.07028056929770.345085055546-0.0493170781192-0.02615632049540.539937540218-0.0169778271410.4348096801139.46428290064-49.8911742214-30.1879123771
52.439951196942.82777601022.815457917229.230157372715.979637498174.50812613762-0.00518148039009-0.003170445426380.3921743965350.4640157561780.0546955061399-0.513469119627-0.4041864940520.104530618234-0.01889841309210.433207773227-0.00892832832169-0.04109817001680.4090067919070.03317342331390.41153284798215.5104913216-27.6398697939-19.2940533129
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 110 )2 - 1101 - 109
22chain 'A' and (resid 111 through 221 )111 - 221110 - 209
33chain 'A' and (resid 222 through 256 )222 - 256210 - 244
44chain 'A' and (resid 257 through 301 )257 - 301245 - 282
55chain 'A' and (resid 302 through 320 )302 - 320283 - 301

+
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