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- PDB-4lfm: Crystal Structure of D-galactose-6-phosphate isomerase in complex... -

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Basic information

Entry
Database: PDB / ID: 4lfm
TitleCrystal Structure of D-galactose-6-phosphate isomerase in complex with D-psicose
Components
  • Galactose-6-phosphate isomerase subunit A
  • Galactose-6-phosphate isomerase subunit B
KeywordsISOMERASE / Rossmann-like alpha-beta-alpha sandwich fold / Rossmann Fold / Sugar-phosphate Binding / Isomerization
Function / homologyRibose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta / D-psicose / : / :
Function and homology information
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJung, W.S. / Pan, C.H.
CitationJournal: Plos One / Year: 2013
Title: Crystal structure and substrate specificity of D-galactose-6-phosphate isomerase complexed with substrates.
Authors: Jung, W.S. / Singh, R.K. / Lee, J.K. / Pan, C.H.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose-6-phosphate isomerase subunit A
B: Galactose-6-phosphate isomerase subunit B
C: Galactose-6-phosphate isomerase subunit A
D: Galactose-6-phosphate isomerase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9086
Polymers73,5474
Non-polymers3602
Water3,585199
1
A: Galactose-6-phosphate isomerase subunit A
B: Galactose-6-phosphate isomerase subunit B
C: Galactose-6-phosphate isomerase subunit A
D: Galactose-6-phosphate isomerase subunit B
hetero molecules

A: Galactose-6-phosphate isomerase subunit A
B: Galactose-6-phosphate isomerase subunit B
C: Galactose-6-phosphate isomerase subunit A
D: Galactose-6-phosphate isomerase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,81512
Polymers147,0958
Non-polymers7214
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area23500 Å2
ΔGint-121 kcal/mol
Surface area42770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.255, 115.958, 54.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Galactose-6-phosphate isomerase subunit A / LacA


Mass: 17884.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: Lc 705 / Gene: lacA, LC705_00641 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7TGZ6, EC: 5.3.1.26
#2: Protein Galactose-6-phosphate isomerase subunit B


Mass: 18889.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: Lc 705 / Gene: lacB, LC705_00640 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7TGZ5, EC: 5.3.1.26
#3: Sugar ChemComp-PSJ / D-psicose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.34 Å3/Da / Density % sol: 47.33 % / Mosaicity: 0.607 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M potassium formate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 82373 / % possible obs: 98.5 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.096 / Χ2: 1.268 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.6810.70.56140210.689196.8
1.68-1.7112.30.50940720.714198.5
1.71-1.7412.60.43340290.742198.8
1.74-1.7812.60.36840810.794198.8
1.78-1.8212.60.32241100.822199.5
1.82-1.8612.70.2840930.871199
1.86-1.912.70.23641260.939199.3
1.9-1.9612.70.19940881.03199.1
1.96-2.01130.17641221.122199.4
2.01-2.08130.15741261.21199.7
2.08-2.15130.14241391.3199.8
2.15-2.2413.10.1341621.399199.8
2.24-2.3413.20.12241371.482199.8
2.34-2.4613.40.11341941.518199.7
2.46-2.6213.60.10541741.623199.8
2.62-2.8213.80.09741641.672199.9
2.82-3.1114.10.0942221.793199.7
3.11-3.55140.08141911.883199
3.55-4.4812.90.07441031.894195.5
4.48-5012.40.06340191.419189.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LFK

4lfk


Resolution: 1.65→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.2474 7643 9.1 %
Rwork0.2269 --
obs-76510 91.5 %
Solvent computationBsol: 23.67 Å2
Displacement parametersBiso max: 58.59 Å2 / Biso mean: 24.0015 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å20 Å2
2---0.839 Å20 Å2
3---2.999 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 24 199 5065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1281.5
X-RAY DIFFRACTIONc_scbond_it1.8082
X-RAY DIFFRACTIONc_mcangle_it1.6392
X-RAY DIFFRACTIONc_scangle_it2.5812.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param
X-RAY DIFFRACTION6psj.param

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