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- PDB-3m9y: Crystal structure of Triosephosphate isomerase from methicillin r... -

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Basic information

Entry
Database: PDB / ID: 3m9y
TitleCrystal structure of Triosephosphate isomerase from methicillin resistant Staphylococcus aureus at 1.9 Angstrom resolution
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM barrel / glycolysis / Gluconeogenesis / Pentose shunt
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
CITRIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMukherjee, S. / Dutta, D. / Saha, B. / 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
DepositionMar 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 17, 2012Group: Database references / Other
Revision 1.3Jun 26, 2013Group: Database references
Revision 1.4Nov 1, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)54,9965
Polymers54,7582
Non-polymers2383
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-25 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.478, 79.478, 175.006
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-297-

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
11THRTHRTHRTHRAA3 - 1074 - 108
21THRTHRTHRTHRBB3 - 1074 - 108
12GLUGLULEULEUAA110 - 156111 - 157
22GLUGLULEULEUBB110 - 156111 - 157
13GLNGLNTRPTRPAA160 - 172161 - 173
23GLNGLNTRPTRPBB160 - 172161 - 173
14ASNASNVALVALAA186 - 242187 - 243
24ASNASNVALVALBB186 - 242187 - 243

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Components

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


Mass: 27378.756 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 / References: UniProt: Q6GIL6, triose-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.52 Å3/Da / Density % sol: 51.26 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M TRISODIUM CITRATE DIHYDRATE, 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: Oct 10, 2009 / Details: Varimax mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→72.365 Å / Num. all: 44961 / Num. obs: 44961 / % possible obs: 99.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 5.5 / Num. unique all: 6332 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BTM

2btm


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.881 / SU B: 6.189 / SU ML: 0.083 / SU R Cruickshank DPI: 0.127 / SU Rfree: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2258 5 %RANDOM
Rwork0.159 ---
obs0.161 44825 99.53 %-
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 max: 80.2 Å2 / Biso mean: 31.097 Å2 / Biso min: 8.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--1.1 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 15 481 4321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223916
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9655298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13726.374171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7915702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3361513
X-RAY DIFFRACTIONr_chiral_restr0.150.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212923
X-RAY DIFFRACTIONr_mcbond_it1.2751.52514
X-RAY DIFFRACTIONr_mcangle_it2.1742.54043
X-RAY DIFFRACTIONr_scbond_it5.31651402
X-RAY DIFFRACTIONr_scangle_it8.335101251
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
884TIGHT POSITIONAL0.10.05
776MEDIUM POSITIONAL0.130.5
884TIGHT THERMAL1.211.5
776MEDIUM THERMAL1.452.5
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 171 -
Rwork0.205 2972 -
all-3143 -
obs--96.26 %
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)
11.5165-0.03390.01490.59290.28211.38150.03380.28160.1546-0.11880.0555-0.1667-0.11010.2647-0.08930.0272-0.01760.0360.129-0.00650.074456.249513.0326-8.0317
20.6811-0.18420.10970.92650.54532.0168-0.0207-0.0670.09310.0033-0.02010.0436-0.1309-0.11270.04080.01250.0053-0.00550.0251-0.01830.042934.711219.661117.4992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 253
2X-RAY DIFFRACTION2B0 - 253

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