[English] 日本語
Yorodumi
- PDB-4amv: E.COLI GLUCOSAMINE-6P SYNTHASE IN COMPLEX WITH FRUCTOSE-6P -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4amv
TitleE.COLI GLUCOSAMINE-6P SYNTHASE IN COMPLEX WITH FRUCTOSE-6P
ComponentsGLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
KeywordsTRANSFERASE / AMMONIA CHANNELING / GLUCOSAMINE 6- PHOSPHATE SYNTHASE / N TERMINAL NUCLEOPHILE / GLUTAMINE AMIDOTRANSFERASE
Function / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FRUCTOSE -6-PHOSPHATE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMouilleron, S. / Golinelli-Pimpaneau, B.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Glutamine Binding Opens the Ammonia Channel and Activates Glucosamine-6P Synthase
Authors: Mouilleron, S. / Badet-Denisot, M.A. / Golinelli-Pimpaneau, B.
#1: Journal: Protein Sci. / Year: 2007
Title: Domain Motions of Glucosamine-6P Synthase: Comparison of the Anisotropic Displacements in the Crystals and the Catalytic Hinge-Bending Rotation.
Authors: Mouilleron, S. / Golinelli-Pimpaneau, B.
#2: Journal: J.Mol.Biol. / Year: 2008
Title: Ordering of C-Terminal Loop and Glutaminase Domains of Glucosamine-6-Phosphate Synthase Promotes Sugar Ring Opening and Formation of the Ammonia Channel.
Authors: Mouilleron, S. / Badet-Denisot, M. / Golinelli-Pimpaneau, B.
#3: Journal: Arch.Biochem.Biophys. / Year: 2011
Title: Dynamics of Glucosamine-6-Phosphate Synthase Catalysis.
Authors: Mouilleron, S. / Badet-Denisot, M. / Badet, B. / Golinelli-Pimpaneau, B.
History
DepositionMar 14, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionApr 24, 2013ID: 2BPL
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
B: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
C: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,6286
Polymers200,8483
Non-polymers7803
Water12,502694
1
A: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
hetero molecules

A: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4194
Polymers133,8982
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7200 Å2
ΔGint-19.1 kcal/mol
Surface area41780 Å2
MethodPISA
2
B: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
C: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4194
Polymers133,8982
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-21.3 kcal/mol
Surface area41470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.197, 109.677, 176.332
Angle α, β, γ (deg.)90.00, 97.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2088-

HOH

21A-2250-

HOH

-
Components

#1: Protein GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING] / D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE / GFAT / GLUCOSAMINE- 6-PHOSPHATE SYNTHASE / ...D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE / GFAT / GLUCOSAMINE- 6-PHOSPHATE SYNTHASE / HEXOSEPHOSPHATE AMINOTRANSFERASE / L-GLUTAMINE- D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE


Mass: 66949.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101
References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 151822

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.8 % / Description: NONE
Crystal growpH: 7.5
Details: 3% PEG 400, 0.1 M HEPES PH 7.5, 0.8 M LICL, 0.01 M FRUCTOSE-6P

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 151822 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.45 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.75
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.62 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JXA CHAIN A

1jxa


Resolution: 2.05→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.238 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23992 7769 5 %RANDOM
Rwork0.2058 ---
obs0.20755 146279 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.557 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å21.02 Å2
2---0.39 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13483 0 48 694 14225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01913748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.96718650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34651821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26124.26561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.531152228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2611583
X-RAY DIFFRACTIONr_chiral_restr0.1710.22165
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110350
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 553 -
Rwork0.335 10277 -
obs--97.3 %
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)
13.04560.22460.0062.3031-0.5423.59270.0049-0.4453-0.17290.3452-0.0477-0.0620.08730.09650.04280.0835-0.0635-0.05130.31950.03740.291228.69723.493994.8561
21.40940.0415-0.11841.44350.32231.2674-0.12220.1727-0.0958-0.18390.1261-0.1273-0.03310.1063-0.00380.0355-0.04840.02210.1731-0.02850.208-2.3707-2.197875.5623
35.37871.3803-1.48175.0146-0.69656.9424-0.20380.0397-0.4133-0.06150.05570.59771.8849-0.95210.1482.5331-0.44270.04770.3657-0.21960.346450.2601-53.482411.4685
40.8456-0.1277-0.63552.28541.62795.84180.0450.27060.171-0.48660.0921-0.25030.8815-0.1208-0.1371.0107-0.1630.04940.3167-0.00480.249856.3808-19.391923.22
51.80870.628-0.66733.1523-0.26863.3238-0.02710.08840.0912-0.32690.1575-0.14490.2015-0.2224-0.13040.1027-0.1127-0.02510.2288-0.06860.255850.57119.456361.5068
61.3471-0.3128-0.78532.25880.59293.2221-0.08180.2289-0.0142-0.2046-0.09360.54060.8856-0.96550.17540.7508-0.4622-0.09260.6391-0.08520.351835.8207-19.272443.6147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 234
2X-RAY DIFFRACTION2A238 - 608
3X-RAY DIFFRACTION2A1609
4X-RAY DIFFRACTION3B1 - 234
5X-RAY DIFFRACTION4B238 - 608
6X-RAY DIFFRACTION4B1609
7X-RAY DIFFRACTION5C1 - 234
8X-RAY DIFFRACTION6C238 - 608
9X-RAY DIFFRACTION6C1609

+
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