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- PDB-2pp3: Crystal structure of L-talarate/galactarate dehydratase mutant K1... -

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Basic information

Entry
Database: PDB / ID: 2pp3
TitleCrystal structure of L-talarate/galactarate dehydratase mutant K197A liganded with Mg and L-glucarate
ComponentsL-talarate/galactarate dehydratase
KeywordsLYASE / Enolase superfamily / L-talarate/Galactarate Dehydratase
Function / homology
Function and homology information


L-talarate dehydratase / L-altrarate catabolic process / L-altrarate dehydratase activity / galactarate dehydratase / galactarate catabolic process / galactarate dehydratase activity / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
L-talarate/galactarate dehydratase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...L-talarate/galactarate dehydratase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-GLUCARIC ACID / L-talarate/galactarate dehydratase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Yew, W.S. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2007
Title: Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2.
Authors: Yew, W.S. / Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-talarate/galactarate dehydratase
B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7769
Polymers132,0723
Non-polymers7036
Water5,459303
1
B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5176
Polymers88,0482
Non-polymers4694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-50 kcal/mol
Surface area27910 Å2
MethodPISA
2
A: L-talarate/galactarate dehydratase
hetero molecules

A: L-talarate/galactarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5176
Polymers88,0482
Non-polymers4694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area7070 Å2
ΔGint-43 kcal/mol
Surface area27520 Å2
MethodPISA
3
B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules

B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules

B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,55218
Polymers264,1456
Non-polymers1,40712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area45520 Å2
ΔGint-217 kcal/mol
Surface area94260 Å2
MethodPISA
4
A: L-talarate/galactarate dehydratase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)265,55218
Polymers264,1456
Non-polymers1,40712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area45880 Å2
ΔGint-186 kcal/mol
Surface area92470 Å2
MethodPISA
5
A: L-talarate/galactarate dehydratase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)354,06924
Polymers352,1938
Non-polymers1,87616
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
MethodPQS
6
B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules

B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules

B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules

B: L-talarate/galactarate dehydratase
C: L-talarate/galactarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,06924
Polymers352,1938
Non-polymers1,87616
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)174.234, 174.234, 123.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
DetailsThe biological assembly is a dimer

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Components

#1: Protein L-talarate/galactarate dehydratase


Mass: 44024.145 Da / Num. of mol.: 3 / Mutation: K197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZL58
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-LGT / L-GLUCARIC ACID / Saccharic acid


Mass: 210.139 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 3.55 Å3/Da / Density % sol: 65.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6 M AmS, 0.1 M Tris HCL , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 83947 / Num. obs: 83947 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.074

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PP0

2pp0


Resolution: 2.2→24.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 186815.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4281 5.1 %RANDOM
Rwork0.204 ---
obs0.204 83947 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1221 Å2 / ksol: 0.375054 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å20 Å20 Å2
2--3.34 Å20 Å2
3----6.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9231 0 45 303 9579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.293 364 5.1 %
Rwork0.258 6831 -
obs--75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4LGT_par.txt&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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