[English] 日本語
Yorodumi
- PDB-1j5x: Crystal structure of Glucosamine-6-phosphate deaminase (TM0813) f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j5x
TitleCrystal structure of Glucosamine-6-phosphate deaminase (TM0813) from Thermotoga maritima at 1.8 A resolution
ComponentsGLUCOSAMINE-6-PHOSPHATE DEAMINASE
KeywordsHYDROLASE / STRUCTURAL GENOMICS / TM0813 / GLUCOSAMINE-6-PHOSPHATE DEAMINASE / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding
Similarity search - Function
GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Glucosamine-6-phosphate deaminase (TM0813) from Thermotoga maritima at 1.8 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Theoretical massNumber of molelcules
Total (without water)39,3031
Polymers39,3031
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE

A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Theoretical massNumber of molelcules
Total (without water)78,6062
Polymers78,6062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area4680 Å2
ΔGint-24 kcal/mol
Surface area21840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.96, 72.96, 128.52
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-401-

HOH

31A-485-

HOH

41A-617-

HOH

-
Components

#1: Protein GLUCOSAMINE-6-PHOSPHATE DEAMINASE /


Mass: 39302.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZS0, glucosamine-6-phosphate deaminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.51 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / pH: 8
Details: 40% PEG-400, 0.1 M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 8.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97980, 0.93218, 0.97999
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.932181
30.979991
ReflectionResolution: 1.7→45.054 Å / Num. obs: 39495 / % possible obs: 99.5 % / Redundancy: 18.3 % / Biso Wilson estimate: 23.99 Å2 / Rsym value: 0.07 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.506 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
CCP4model building
SOLVEphasing
RESOLVEmodel building
CNS1refinement
CCP4(SCALA)data scaling
CCP4phasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1914 4.8 %RANDOM
Rwork0.192 ---
obs0.192 37360 100 %-
all-37372 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 0.37 Å2 / ksol: 64.8 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.173 Å2-1.479 Å20 Å2
2---4.173 Å20 Å2
3---8.345 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 0 294 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.94
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.9351.5
X-RAY DIFFRACTIONc_mcangle_it2.5122
X-RAY DIFFRACTIONc_scbond_it3.2242
X-RAY DIFFRACTIONc_scangle_it4.1412.5
LS refinement shellResolution: 1.8→1.82 Å / Total num. of bins used: 38
RfactorNum. reflection% reflection
Rfree0.2985 47 4.9 %
Rwork0.2432 912 -

+
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