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- PDB-3uwz: Crystal structure of Staphylococcus aureus triosephosphate isomer... -

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Basic information

Entry
Database: PDB / ID: 3uwz
TitleCrystal structure of Staphylococcus aureus triosephosphate isomerase complexed with glycerol-2-phosphate
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
Chem-G2H / PHOSPHATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,9685
Polymers56,5292
Non-polymers4393
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-41 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.022, 79.022, 174.956
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
11THRTHRPHEPHEAA3 - 7011 - 78
21THRTHRPHEPHEBB3 - 7011 - 78
12ASPASPPHEPHEAA72 - 10480 - 112
22ASPASPPHEPHEBB72 - 10480 - 112
13ILEILETHRTHRAA111 - 132119 - 140
23ILEILETHRTHRBB111 - 132119 - 140
14LYSLYSSERSERAA140 - 180148 - 188
24LYSLYSSERSERBB140 - 180148 - 188
15ALAALALYSLYSAA185 - 241193 - 249
25ALAALALYSLYSBB185 - 241193 - 249
16LEULEUGLYGLYAA249 - 251257 - 259
26LEULEUGLYGLYBB249 - 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: Chemical ChemComp-G2H / 2-HYDROXY-1-(HYDROXYMETHYL)ETHYL DIHYDROGEN PHOSPHATE / GLYCEROL-2-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
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: Sep 26, 2010 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.497→72.017 Å / Num. obs: 19971 / % possible obs: 99.5 % / Redundancy: 14 % / Rsym value: 0.086 / Net I/σ(I): 27.4
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.524 / % possible all: 99

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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: 2.5→29.66 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.592 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.571 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1016 5.1 %RANDOM
Rwork0.19 ---
obs0.192 18891 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--1.58 Å20 Å2
3----3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 25 147 3987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223911
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.9685290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6715507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15826.491171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83315700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7561512
X-RAY DIFFRACTIONr_chiral_restr0.0620.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212898
X-RAY DIFFRACTIONr_mcbond_it0.3821.52502
X-RAY DIFFRACTIONr_mcangle_it0.8092.54024
X-RAY DIFFRACTIONr_scbond_it2.29851409
X-RAY DIFFRACTIONr_scangle_it4.121101263
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
882tight positional0.030.05
764medium positional0.030.5
882tight thermal0.191.5
764medium thermal0.322.5
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 97 -
Rwork0.231 1340 -
obs--98.63 %
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)
11.0567-0.58790.28791.9457-1.11933.07950.0553-0.078-0.14050.0418-0.0389-0.05680.09430.1986-0.01640.01320.0038-0.01240.03130.02530.04724.472419.830217.1303
22.44740.30120.14551.2794-0.49142.4280.04650.3316-0.1645-0.18370.0890.17340.1843-0.3327-0.13560.0361-0.0154-0.02920.11680.00350.0659-16.742926.5632-8.2086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 253
2X-RAY DIFFRACTION2B1 - 253

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