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

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Basic information

Entry
Database: PDB / ID: 3uwu
TitleCrystal structure of Staphylococcus Aureus triosephosphate isomerase complexed with glycerol-3-phosphate
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM BARREL
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
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
CITRIC ACID / SN-GLYCEROL-3-PHOSPHATE / Triosephosphate isomerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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)57,0665
Polymers56,5292
Non-polymers5363
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-35 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.100, 81.100, 174.600
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
11THRTHRLYSLYSAA3 - 3311 - 41
21THRTHRLYSLYSBB3 - 3311 - 41
12VALVALPHEPHEAA35 - 7043 - 78
22VALVALPHEPHEBB35 - 7043 - 78
13ASNASNGLUGLUAA73 - 10681 - 114
23ASNASNGLUGLUBB73 - 10681 - 114
14ILEILEPHEPHEAA111 - 119119 - 127
24ILEILEPHEPHEBB111 - 119119 - 127
15HISHISTHRTHRAA121 - 132129 - 140
25HISHISTHRTHRBB121 - 132129 - 140
16GLYGLYSERSERAA139 - 157147 - 165
26GLYGLYSERSERBB139 - 157147 - 165
17GLNGLNALAALAAA160 - 185168 - 193
27GLNGLNALAALABB160 - 185168 - 193
18CYSCYSSERSERAA189 - 201197 - 209
28CYSCYSSERSERBB189 - 201197 - 209
19SERSERSERSERAA205 - 215213 - 223
29SERSERSERSERBB205 - 215213 - 223
110LYSLYSLYSLYSAA217 - 241225 - 249
210LYSLYSLYSLYSBB217 - 241225 - 249
111ASPASPLEULEUAA244 - 249252 - 257
211ASPASPLEULEUBB244 - 249252 - 257

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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-G3P / SN-GLYCEROL-3-PHOSPHATE / Glycerol 3-phosphate


Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M TRI-SODIUM 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 24, 2010 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.149→73.553 Å / Num. obs: 32236 / % possible obs: 98.7 % / Redundancy: 13 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.102 / Net I/σ(I): 19.5
Reflection shellResolution: 2.15→2.26 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.439 / % possible all: 91.7

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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: 2.15→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.495 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1628 5.1 %RANDOM
Rwork0.181 ---
obs0.183 32120 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2--1.17 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 33 376 4224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223923
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9695311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0885511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98326.491171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97215696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7571512
X-RAY DIFFRACTIONr_chiral_restr0.0720.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212922
X-RAY DIFFRACTIONr_mcbond_it0.4241.52509
X-RAY DIFFRACTIONr_mcangle_it0.8812.54036
X-RAY DIFFRACTIONr_scbond_it2.72751414
X-RAY DIFFRACTIONr_scangle_it4.678101271
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
885tight positional0.040.05
757medium positional0.040.5
885tight thermal0.291.5
757medium thermal0.482.5
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 100 -
Rwork0.2 1898 -
obs--85.68 %
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)
10.7605-0.19690.00830.7153-0.16371.21980.0423-0.1064-0.02780.0242-0.0347-0.05470.05360.1329-0.00760.0113-0.00220.00590.05230.0020.04755.368320.26417.0752
21.16460.2091-0.2120.846-0.09371.19850.02340.15050.0283-0.16140.02720.0827-0.0098-0.1929-0.05050.04390.01380.00160.06560.01220.0481-15.80728.1051-7.9621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 253
2X-RAY DIFFRACTION2B1 - 252

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