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- PDB-2htb: Crystal Structure of a putative mutarotase (YeaD) from Salmonella... -

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Basic information

Entry
Database: PDB / ID: 2htb
TitleCrystal Structure of a putative mutarotase (YeaD) from Salmonella typhimurium in monoclinic form
ComponentsPutative enzyme related to aldose 1-epimerase
KeywordsISOMERASE / Salmonella typhimurium / carbohydrate / aldose 1-epimerase / mutarotase / YeaD / GalM / sugar phosphate
Function / homology
Function and homology information


glucose-6-phosphate 1-epimerase / glucose-6-phosphate 1-epimerase activity / carbohydrate binding / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Glucose-6-phosphate 1-epimerase / Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative glucose-6-phosphate 1-epimerase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChittori, S. / Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the putative mutarotase YeaD from Salmonella typhimurium: structural comparison with galactose mutarotases.
Authors: Chittori, S. / Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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

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Assembly

Deposited unit
A: Putative enzyme related to aldose 1-epimerase
B: Putative enzyme related to aldose 1-epimerase
C: Putative enzyme related to aldose 1-epimerase
D: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)137,3754
Polymers137,3754
Non-polymers00
Water5,801322
1
A: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)34,3441
Polymers34,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)34,3441
Polymers34,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)34,3441
Polymers34,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)34,3441
Polymers34,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.553, 47.599, 138.086
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative enzyme related to aldose 1-epimerase


Mass: 34343.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: IFO12529 / Gene: yeaD / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
References: UniProt: Q8ZPV9, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15-25% PEG8K, 0.1M citrate pH 5.5, 0.2-0.5mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 13, 2005 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 50200 / % possible obs: 0.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.22 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4503 / % possible all: 0.919

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: monomer of orthorhombic form of stYeaD (PDB code 2HTA)

2hta


Resolution: 2.5→27.8 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.525 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23974 2480 5 %RANDOM
Rwork0.18877 ---
all0.19135 50310 --
obs0.19135 47276 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.472 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.02 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9112 0 0 322 9434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0219357
X-RAY DIFFRACTIONr_angle_refined_deg2.3141.93712794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.60251179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06724.269417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.629151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8961545
X-RAY DIFFRACTIONr_chiral_restr0.1570.21445
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027231
X-RAY DIFFRACTIONr_nbd_refined0.2380.24232
X-RAY DIFFRACTIONr_nbtor_refined0.3250.26246
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2532
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.28
X-RAY DIFFRACTIONr_mcbond_it1.7341.56046
X-RAY DIFFRACTIONr_mcangle_it2.17429540
X-RAY DIFFRACTIONr_scbond_it3.98633764
X-RAY DIFFRACTIONr_scangle_it5.5484.53254
LS refinement shellResolution: 2.499→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 153 -
Rwork0.319 3108 -
obs--91.01 %

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