[English] 日本語
Yorodumi
- PDB-1ni9: 2.0 A structure of glycerol metabolism protein from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ni9
Title2.0 A structure of glycerol metabolism protein from E. coli
ComponentsProtein glpX
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain structure of two alpha/beta folds / Extended beta sheets / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


glycerol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / manganese ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #90 / Fructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase / Bacterial fructose-1,6-bisphosphatase, glpX-encoded / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fructose-1,6-bisphosphatase 1 class 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSanishvili, R. / Brunzelle, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Biochemical Characterization of the Type II Fructose-1,6-bisphosphatase GlpX from Escherichia coli.
Authors: Brown, G. / Singer, A. / Lunin, V.V. / Proudfoot, M. / Skarina, T. / Flick, R. / Kochinyan, S. / Sanishvili, R. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Yakunin, A.F.
History
DepositionDec 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE AUTHORS STATE THE BIOLOGICAL UNIT IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein glpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2833
Polymers36,0911
Non-polymers1922
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.453, 61.453, 171.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Protein glpX


Mass: 36090.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLPX OR B3925 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9C9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 %PEG80001reservoir
20.2 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoirpH4.4

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9793, 0.9795
SYNCHROTRONAPS 19-ID21.0332
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDApr 22, 2002mirror
CUSTOM-MADE2CCDDec 19, 2001mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Sagittally focusing double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Sagittally focusing double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
31.03321
ReflectionResolution: 2→50 Å / Num. obs: 22955 / Rsym value: 0.66
Reflection shellHighest resolution: 2 Å / Num. unique all: 2102 / Rsym value: 0.327
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99.8 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / % possible obs: 98.1 % / Redundancy: 8 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
d*TREKdata reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.317 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 1095 5.1 %RANDOM
Rwork0.18656 ---
obs0.18934 20446 93.11 %-
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: 22.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2--1.05 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 10 143 2345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222218
X-RAY DIFFRACTIONr_bond_other_d0.0020.022182
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9873002
X-RAY DIFFRACTIONr_angle_other_deg0.95235036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022436
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02412
X-RAY DIFFRACTIONr_nbd_refined0.2050.2443
X-RAY DIFFRACTIONr_nbd_other0.2490.22587
X-RAY DIFFRACTIONr_nbtor_other0.090.21548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0011.51441
X-RAY DIFFRACTIONr_mcangle_it1.75222310
X-RAY DIFFRACTIONr_scbond_it2.6723777
X-RAY DIFFRACTIONr_scangle_it4.3564.5692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 54
Rwork0.241 1224
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)
10.44220.0502-0.55580.2659-0.21611.29460.00050.0723-0.0499-0.0576-0.00510.03570.057-0.08970.00450.0048-0.008900.0177-0.00540.028424.877810.823446.5481
20.36020.2047-0.55660.0511-0.24721.02610.01060.0322-0.0007-0.0125-0.0072-0.01130.0237-0.0373-0.00340.0523-0.0061-0.0120.049-0.00480.078825.230411.895550.7452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3263 - 328
2X-RAY DIFFRACTION2AD - C402 - 4011
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 39 Å / Num. reflection obs: 34514 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.43

+
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