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- PDB-3uwy: Crystal structure of triosephosphate isomerase from Methicillin r... -

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Basic information

Entry
Database: PDB / ID: 3uwy
TitleCrystal structure of triosephosphate isomerase from Methicillin resistant Staphylococcus Aureus at 2.4 angstrom resolution
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM BARREL / CYTOSOL
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Triosephosphate isomerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMukherjee, S. / Roychowdhury, A. / Dutta, D. / Das, A.K.
CitationJournal: Biochimie / Year: 2012
Title: Crystal structures of triosephosphate isomerase from methicillin resistant Staphylococcus aureus MRSA252 provide structural insights into novel modes of ligand binding and unique conformations of catalytic loop
Authors: Mukherjee, S. / Roychowdhury, A. / Dutta, D. / Das, A.K.
History
DepositionDec 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)56,5292
Polymers56,5292
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-24 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.624, 76.624, 174.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRARGARGAA3 - 10011 - 108
21THRTHRARGARGBB3 - 10011 - 108
12ILEILEPHEPHEAA111 - 119119 - 127
22ILEILEPHEPHEBB111 - 119119 - 127
13HISHISGLUGLUAA121 - 135129 - 143
23HISHISGLUGLUBB121 - 135129 - 143
14GLYGLYASNASNAA139 - 142147 - 150
24GLYGLYASNASNBB139 - 142147 - 150
15VALVALGLUGLUAA149 - 169157 - 177
25VALVALGLUGLUBB149 - 169157 - 177
16SERSERSERSERAA180 - 200188 - 208
26SERSERSERSERBB180 - 200188 - 208
17SERSERLYSLYSAA205 - 222213 - 230
27SERSERLYSLYSBB205 - 222213 - 230
18TYRTYRALAALAAA224 - 226232 - 234
28TYRTYRALAALABB224 - 226232 - 234
19ILEILELYSLYSAA230 - 241238 - 249
29ILEILELYSLYSBB230 - 241238 - 249
110LEULEUGLYGLYAA249 - 251257 - 259
210LEULEUGLYGLYBB249 - 251257 - 259

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Components

#1: Protein Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 28264.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: SAR0830, tpi, tpiA / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 (PREP4) / References: UniProt: Q6GIL6, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 16, 2010 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.396→70.172 Å / Num. obs: 21249 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.125 / Net I/σ(I): 14.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.556 / % possible all: 99.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.5.0095refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M9Y

3m9y


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.869 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1084 5.1 %RANDOM
Rwork0.177 ---
obs0.18 21067 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 0 191 4085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223966
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.9545365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8015516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30826.25176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38215703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.961512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212970
X-RAY DIFFRACTIONr_mcbond_it0.4551.52547
X-RAY DIFFRACTIONr_mcangle_it0.9422.54093
X-RAY DIFFRACTIONr_scbond_it2.56351419
X-RAY DIFFRACTIONr_scangle_it4.588101270
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
815tight positional0.040.05
694medium positional0.040.5
815tight thermal0.221.5
694medium thermal0.362.5
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 83 -
Rwork0.213 1410 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.27180.30460.50911.08390.00891.63480.06250.0317-0.0518-0.07050.02130.04990.0378-0.0354-0.08380.015-0.00320.00040.0067-0.00490.02332.814157.816326.9348
22.3334-0.77950.13031.48970.39261.7433-0.0342-0.26660.01060.15880.1071-0.17740.01380.1653-0.07290.0352-0.0192-0.00210.0784-0.02670.056855.377365.178951.5052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 253
2X-RAY DIFFRACTION2B1 - 253

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