[English] 日本語
Yorodumi
- PDB-4qih: The structure of mycobacterial glucosyl-3-phosphoglycerate phosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qih
TitleThe structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase Rv2419c complexes with VO3
ComponentsGlucosyl-3-phosphoglycerate phosphatase
KeywordsHYDROLASE / glycosyl-3-phosphoglycerate / glycolysis
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase activity
Similarity search - Function
Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / Glucosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsZhou, W.H. / Zheng, Q.Q. / Jiang, D.Q. / Zhang, W. / Zhang, Q.Q. / Jin, J. / Li, X. / Yang, H.T. / Shaw, N. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanism of dephosphorylation of glucosyl-3-phosphoglycerate by a histidine phosphatase
Authors: Zheng, Q. / Jiang, D. / Zhang, W. / Zhang, Q. / Zhao, Q. / Jin, J. / Li, X. / Yang, H. / Bartlam, M. / Shaw, N. / Zhou, W. / Rao, Z.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Nov 8, 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 / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Glucosyl-3-phosphoglycerate phosphatase
B: Glucosyl-3-phosphoglycerate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6064
Polymers48,4092
Non-polymers1982
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.312, 82.762, 131.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glucosyl-3-phosphoglycerate phosphatase / / GpgP / Mannosyl-3-phosphoglycerate phosphatase / MpgP / Glucosyl-3-phosphoglycerate phosphatase / ...GpgP / Mannosyl-3-phosphoglycerate phosphatase / MpgP / Glucosyl-3-phosphoglycerate phosphatase / GpgP / Mannosyl-3-phosphoglycerate phosphatase / MpgP


Mass: 24204.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gpgP, MT2492, Rv2419c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P9WIC6, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, mannosyl-3-phosphoglycerate phosphatase
#2: Chemical ChemComp-VN3 / VANADATE ION / METAVANADATE / Vanadate


Mass: 98.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium pH7.5, 10% 2-propanol, 20% w/v polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.03935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2013
Details: Double crystal Monochromator with Si (111) numerical link type. Mirror 1: colli mating, Rh-coated silicon single crystal, flat shaped. Mirror 2: focusing, Rh-co ated silicon single crystal, Toroidal.roidal.
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03935 Å / Relative weight: 1
ReflectionResolution: 2.299→50 Å / Num. all: 23222 / Num. obs: 22409 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.055 / Rsym value: 0.05 / Net I/σ(I): 46
Reflection shellResolution: 2.299→2.34 Å / Redundancy: 7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 9 / Num. unique all: 1128 / Rsym value: 0.22 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PZ9

4pz9


Resolution: 2.299→35.008 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 2000 8.95 %RANDOM
Rwork0.1868 ---
obs0.192 22339 96.37 %-
all-23180 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.299→35.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 8 126 3285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143223
X-RAY DIFFRACTIONf_angle_d1.4934381
X-RAY DIFFRACTIONf_dihedral_angle_d14.8231158
X-RAY DIFFRACTIONf_chiral_restr0.065488
X-RAY DIFFRACTIONf_plane_restr0.009570
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2993-2.35680.30641430.2098145599
2.3568-2.42050.26241460.20531488100
2.4205-2.49170.26911450.20241473100
2.4917-2.57210.30391480.18811512100
2.5721-2.6640.26661420.20031447100
2.664-2.77070.28461480.21361499100
2.7707-2.89670.30661480.21491508100
2.8967-3.04930.29131460.22131478100
3.0493-3.24030.27721460.21431497100
3.2403-3.49020.27561490.21011511100
3.4902-3.84110.2589890.204889459
3.8411-4.3960.21421370.1582139992
4.396-5.53490.2121540.1491557100
5.5349-35.01240.18061590.1675162199

+
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