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- PDB-2afa: Crystal Structure of putative NAG isomerase from Salmonella typhi... -

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Basic information

Entry
Database: PDB / ID: 2afa
TitleCrystal Structure of putative NAG isomerase from Salmonella typhimurium
ComponentsNAG isomerase
KeywordsISOMERASE / NAG isomerase / Dimer-of-Trimers / renin-binding protein / alpha/alpha-fold / T1489 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


sulfoquinovose isomerase / sulfoquinovose isomerase activity / : / carbohydrate metabolic process
Similarity search - Function
Sulfoquinovose isomerase / AGE domain / N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Sulfoquinovose isomerase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsKumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of putative NAG isomerase from Salmonella typhimurium
Authors: Kumaran, D. / Swaminathan, S.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: NAG isomerase
B: NAG isomerase
C: NAG isomerase
D: NAG isomerase
E: NAG isomerase
F: NAG isomerase


Theoretical massNumber of molelcules
Total (without water)296,4836
Polymers296,4836
Non-polymers00
Water11,908661
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.933, 91.140, 95.102
Angle α, β, γ (deg.)106.81, 103.52, 111.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NAG isomerase


Mass: 49413.785 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: yihS / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZKT7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG, sodium cacodylate, sodium acetate , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 132272 / Num. obs: 132272 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.75 / Num. unique all: 13231 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→45.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 394169.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: In all the chains, residue 416 and residues 376 to 379 were not modelled due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2517 2 %RANDOM
Rwork0.207 ---
obs0.207 126832 95.4 %-
all-126832 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3409 Å2 / ksol: 0.334343 e/Å3
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1-4.43 Å2-0.15 Å21.98 Å2
2---2.13 Å20.35 Å2
3----2.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.15→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19908 0 0 661 20569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 356 1.9 %
Rwork0.284 18374 -
obs--84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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