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- PDB-4lfk: Crystal Structure of D-galactose-6-phosphate isomerase in a subst... -

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Basic information

Entry
Database: PDB / ID: 4lfk
TitleCrystal Structure of D-galactose-6-phosphate isomerase in a substrate-free form
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 / : / :
Function and homology information
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)73,5474
Polymers73,5474
Non-polymers00
Water3,171176
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

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


Theoretical massNumber of molelcules
Total (without water)147,0958
Polymers147,0958
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area23070 Å2
ΔGint-132 kcal/mol
Surface area43180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.174, 115.926, 54.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 47.4 % / Mosaicity: 0.381 °
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: 1.96→50 Å / Num. obs: 50182 / % possible obs: 99.7 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.073 / Χ2: 0.994 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.96-1.9911.70.31923060.737194.1
1.99-2.0313.80.28925130.798199.8
2.03-2.0714.50.25624400.853199.9
2.07-2.1114.50.22525010.8871100
2.11-2.1614.70.2124530.9041100
2.16-2.2114.50.18825220.9311100
2.21-2.2614.70.15924650.9761100
2.26-2.3214.70.15224760.9791100
2.32-2.3914.70.13925040.9821100
2.39-2.4714.80.12524970.9991100
2.47-2.5614.80.10824861.0261100
2.56-2.6614.80.09625101.041100
2.66-2.7814.80.08725031.0641100
2.78-2.9314.80.07725191.081100
2.93-3.1114.80.06725231.0791100
3.11-3.3514.80.05825361.0791100
3.35-3.6914.70.0525401.0851100
3.69-4.2214.60.04525641.0641100
4.22-5.3214.40.04225921.0291100
5.32-5013.60.04527321.194199.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NN4

1nn4


Resolution: 1.96→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.2116 4856 9.6 %
Rwork0.2046 --
obs-47906 95.2 %
Solvent computationBsol: 13.4704 Å2
Displacement parametersBiso max: 71.56 Å2 / Biso mean: 21.3874 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--5.672 Å20 Å20 Å2
2--1.77 Å20 Å2
3---3.901 Å2
Refinement stepCycle: LAST / Resolution: 1.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 0 176 5018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1551.5
X-RAY DIFFRACTIONc_scbond_it1.8642
X-RAY DIFFRACTIONc_mcangle_it1.7072
X-RAY DIFFRACTIONc_scangle_it2.7362.5
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

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