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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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

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