[English] 日本語
Yorodumi
- PDB-5hj5: Crystal structure of tertiary complex of glucosamine-6-phosphate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hj5
TitleCrystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio cholerae with BETA-D-GLUCOSE-6-PHOSPHATE and FRUCTOSE-6-PHOSPHATE
ComponentsGlucosamine-6-phosphate deaminase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / glucosamine-6-phosphate deaminase / Vibrio cholerae
Function / homology
Function and homology information


glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / 6-O-phosphono-beta-D-glucopyranose / FRUCTOSE -6-PHOSPHATE / Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChang, C. / Maltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio cholerae with BETA-D-GLUCOSE-6-PHOSPHATE and FRUCTOSE -6-PHOSPHATE
Authors: Chang, C. / Maltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucosamine-6-phosphate deaminase
B: Glucosamine-6-phosphate deaminase
C: Glucosamine-6-phosphate deaminase
D: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,66119
Polymers118,9684
Non-polymers2,69415
Water21,9961221
1
A: Glucosamine-6-phosphate deaminase
hetero molecules

A: Glucosamine-6-phosphate deaminase
hetero molecules

A: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,61518
Polymers89,2263
Non-polymers2,39015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8670 Å2
ΔGint-35 kcal/mol
Surface area30940 Å2
MethodPISA
2
B: Glucosamine-6-phosphate deaminase
hetero molecules

B: Glucosamine-6-phosphate deaminase
hetero molecules

B: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,24315
Polymers89,2263
Non-polymers2,01712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7220 Å2
ΔGint-32 kcal/mol
Surface area31350 Å2
MethodPISA
3
C: Glucosamine-6-phosphate deaminase
hetero molecules

C: Glucosamine-6-phosphate deaminase
hetero molecules

C: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,06312
Polymers89,2263
Non-polymers1,8379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7140 Å2
ΔGint-35 kcal/mol
Surface area31070 Å2
MethodPISA
4
D: Glucosamine-6-phosphate deaminase
hetero molecules

D: Glucosamine-6-phosphate deaminase
hetero molecules

D: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,06312
Polymers89,2263
Non-polymers1,8379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7380 Å2
ΔGint-33 kcal/mol
Surface area30940 Å2
MethodPISA
5
A: Glucosamine-6-phosphate deaminase
hetero molecules

A: Glucosamine-6-phosphate deaminase
hetero molecules

A: Glucosamine-6-phosphate deaminase
hetero molecules

C: Glucosamine-6-phosphate deaminase
hetero molecules

C: Glucosamine-6-phosphate deaminase
hetero molecules

C: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,67830
Polymers178,4516
Non-polymers4,22724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation4_665-x+1,-y+1,z+1/21
crystal symmetry operation5_565y,-x+y+1,z+1/21
crystal symmetry operation6_555x-y,x,z+1/21
Buried area18810 Å2
ΔGint-72 kcal/mol
Surface area59000 Å2
MethodPISA
6
B: Glucosamine-6-phosphate deaminase
hetero molecules

B: Glucosamine-6-phosphate deaminase
hetero molecules

B: Glucosamine-6-phosphate deaminase
hetero molecules

D: Glucosamine-6-phosphate deaminase
hetero molecules

D: Glucosamine-6-phosphate deaminase
hetero molecules

D: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,30627
Polymers178,4516
Non-polymers3,85421
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area17590 Å2
ΔGint-66 kcal/mol
Surface area59290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.093, 113.093, 215.683
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11C-673-

HOH

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Glucosamine-6-phosphate deaminase / GlcN6P deaminase / GNPDA / Glucosamine-6-phosphate isomerase


Mass: 29741.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: nagB, VC_A1025 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q9KKS5, glucosamine-6-phosphate deaminase
#3: Sugar
ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 1232 molecules

#2: Chemical
ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O9P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1221 / 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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Ammonium acetate, 0.1M Bis-Tris, 17 % PEG1-K, 10 mM Praseodymium(III) acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2015
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 170772 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.81 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.027 / Rrim(I) all: 0.081 / Χ2: 0.937 / Net I/av σ(I): 28.467 / Net I/σ(I): 7.8 / Num. measured all: 1460271
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7360.73585070.7980.3260.8060.685100
1.73-1.767.10.63885670.850.2560.6880.717100
1.76-1.797.70.54385240.8970.2090.5830.732100
1.79-1.838.60.46185010.9280.1670.4910.758100
1.83-1.878.70.38585370.950.1390.4090.795100
1.87-1.918.70.31185470.9650.1120.3310.838100
1.91-1.968.70.26785130.9770.0960.2840.866100
1.96-2.028.80.22385010.9830.080.2370.887100
2.02-2.078.80.18684700.9870.0660.1970.919100
2.07-2.148.80.15785890.9910.0560.1670.947100
2.14-2.228.90.12885510.9930.0450.1350.987100
2.22-2.318.90.1185160.9950.0390.1161100
2.31-2.418.90.185330.9950.0350.1060.972100
2.41-2.5490.08685250.9970.030.0910.955100
2.54-2.78.90.07585590.9970.0260.0790.958100
2.7-2.9190.06685330.9970.0230.070.983100
2.91-3.290.06585250.9970.0230.0691.196100
3.2-3.668.90.06585630.9970.0230.0691.586100
3.66-4.618.80.04785710.9980.0170.051.096100
4.61-508.90.03286400.9990.0120.0350.66699.8

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
SBC-Collectdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R7T

4r7t


Resolution: 1.7→39.023 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.87 / Stereochemistry target values: ML
Details: According to the authors the breaks in peptide linkage between residues 262, 263 and 263, 264 are due to the fact that the coordinates of residues from 259 for molecules C and D are ...Details: According to the authors the breaks in peptide linkage between residues 262, 263 and 263, 264 are due to the fact that the coordinates of residues from 259 for molecules C and D are representing only partial structures among more than 20 multiple conformations.
RfactorNum. reflection% reflection
Rfree0.1697 17059 5.03 %
Rwork0.1354 322113 -
obs0.1371 170600 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.03 Å2 / Biso mean: 25.7582 Å2 / Biso min: 11.75 Å2
Refinement stepCycle: final / Resolution: 1.7→39.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8333 0 184 1221 9738
Biso mean--31.54 37.77 -
Num. residues----1065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069117
X-RAY DIFFRACTIONf_angle_d0.82812395
X-RAY DIFFRACTIONf_chiral_restr0.0521395
X-RAY DIFFRACTIONf_plane_restr0.0051599
X-RAY DIFFRACTIONf_dihedral_angle_d15.7295456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6997-1.71910.29854780.2289105871106597
1.7191-1.73930.23436020.20321080811410100
1.7393-1.76050.25595560.19391064311199100
1.7605-1.78280.22945680.17591076311331100
1.7828-1.80620.21886730.16261062911302100
1.8062-1.8310.19435980.15381077511373100
1.831-1.85710.20485820.14281075511337100
1.8571-1.88490.17736200.14361067111291100
1.8849-1.91430.19335820.14181079211374100
1.9143-1.94570.17396240.13391061111235100
1.9457-1.97920.18795280.12771086811396100
1.9792-2.01520.15275740.11831070811282100
2.0152-2.0540.16085080.12161077811286100
2.054-2.09590.16964960.12361084411340100
2.0959-2.14150.18155760.12861070711283100
2.1415-2.19130.17155620.12471068311245100
2.1913-2.24610.16485560.11681080111357100
2.2461-2.30680.17616160.12161074411360100
2.3068-2.37470.17865660.12651067311239100
2.3747-2.45130.17455920.12491080611398100
2.4513-2.53890.16756100.12281069411304100
2.5389-2.64060.17345920.12791068211274100
2.6406-2.76070.16676160.1341073511351100
2.7607-2.90620.16065180.131079811316100
2.9062-3.08820.17385740.13731071111285100
3.0882-3.32650.16715620.13841079011352100
3.3265-3.66110.1545220.13741076111283100
3.6611-4.19030.1515020.12131084211344100
4.1903-5.27730.1465680.12521072011288100
5.2773-39.03330.15815380.1654107341127299

+
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