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- PDB-3uww: Crystal structure of Staphylococcus Aureus triosephosphate isomer... -

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Basic information

Entry
Database: PDB / ID: 3uww
TitleCrystal structure of Staphylococcus Aureus triosephosphate isomerase complexed with 3-phosphoglyceric acid
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 / glycolytic process / gluconeogenesis / 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
3-PHOSPHOGLYCERIC ACID / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Triosephosphate isomerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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 ...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_ncs_dom_lim / 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_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 / _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

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0796
Polymers56,5292
Non-polymers5494
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-48 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.583, 80.583, 174.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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
11METMETPROPROAA1 - 309 - 38
21ARGARGPROPROBB2 - 3010 - 38
12VALVALLEULEUAA35 - 6143 - 69
22VALVALLEULEUBB35 - 6143 - 69
13ILEILEPHEPHEAA63 - 7071 - 78
23ILEILEPHEPHEBB63 - 7071 - 78
14GLYGLYASPASPAA74 - 10882 - 116
24GLYGLYASPASPBB74 - 10882 - 116
15GLUGLUGLUGLUAA110 - 131118 - 139
25GLUGLUGLUGLUBB110 - 131118 - 139
16ASNASNGLUGLUAA142 - 169150 - 177
26ASNASNGLUGLUBB142 - 169150 - 177
17THRTHRGLUGLUAA181 - 187189 - 195
27THRTHRGLUGLUBB181 - 187189 - 195
18CYSCYSTYRTYRAA189 - 212197 - 220
28CYSCYSTYRTYRBB189 - 212197 - 220
19PROPROASNASNAA218 - 220226 - 228
29PROPROASNASNBB218 - 220226 - 228
110ASPASPLEULEUAA229 - 240237 - 248
210ASPASPLEULEUBB229 - 240237 - 248
111VALVALGLYGLYAA242 - 251250 - 259
211VALVALGLYGLYBB242 - 251250 - 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: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M TRISODIUM CITRATE, pH 6.5, 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: Dec 7, 2010 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.247→73.125 Å / Num. obs: 28110 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.081 / Net I/σ(I): 15.1
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.466 / % possible all: 98.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M9Y

3m9y


Resolution: 2.25→29.56 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.113 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1412 5 %RANDOM
Rwork0.206 ---
obs0.209 26625 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 31 211 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223891
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.9675261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9315503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03126.429168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47715684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5911512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212890
X-RAY DIFFRACTIONr_mcbond_it0.4491.52497
X-RAY DIFFRACTIONr_mcangle_it0.9212.54011
X-RAY DIFFRACTIONr_scbond_it2.41151394
X-RAY DIFFRACTIONr_scangle_it4.343101250
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
820tight positional0.040.05
726medium positional0.040.5
820tight thermal0.381.5
726medium thermal0.442.5
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 94 -
Rwork0.24 1908 -
obs--98.09 %
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)
10.6409-0.12570.04880.7989-0.26551.61630.112-0.1555-0.0283-0.087-0.0540.0061-0.03790.0025-0.0580.0317-0.02750.01370.1379-0.00130.0745.209620.332617.2494
21.56860.1376-0.28470.5218-0.20521.40820.04390.1497-0.0298-0.16680.03020.0513-0.1093-0.3416-0.07410.08190.04550.00470.16690.02680.1065-15.957727.2825-8.0442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 253
2X-RAY DIFFRACTION2B2 - 252

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