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- PDB-1oy0: The crystal Structure of the First Enzyme of Pantothenate Biosynt... -

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Basic information

Entry
Database: PDB / ID: 1oy0
TitleThe crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase from Mycobacterium Tuberculosis Shows a Decameric Assembly and Terminal Helix-Swapping
ComponentsKetopantoate hydroxymethyltransferase
KeywordsTRANSFERASE / domain swapping / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


3-methyl-2-oxobutanoate hydroxymethyltransferase / 3-methyl-2-oxobutanoate hydroxymethyltransferase activity / pantothenate biosynthetic process / magnesium ion binding / plasma membrane / cytoplasm
Similarity search - Function
Ketopantoate hydroxymethyltransferase / Ketopantoate hydroxymethyltransferase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-methyl-2-oxobutanoate hydroxymethyltransferase / 3-methyl-2-oxobutanoate hydroxymethyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SAS with averaging / Resolution: 2.8 Å
AuthorsChaudhuri, B.N. / Sawaya, M.R. / Kim, C.Y. / Waldo, G.S. / Park, M.S. / Terwilliger, T.C. / Yeates, T.O. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2003
Title: The Crystal Structure of the First Enzyme in the Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase, from M. tuberculosis
Authors: Chaudhuri, B.N. / Sawaya, M.R. / Kim, C.Y. / Waldo, G.S. / Park, M.S. / Terwilliger, T.C. / Yeates, T.O.
History
DepositionApr 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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_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_conn.ptnr2_label_seq_id / _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: Ketopantoate hydroxymethyltransferase
B: Ketopantoate hydroxymethyltransferase
C: Ketopantoate hydroxymethyltransferase
D: Ketopantoate hydroxymethyltransferase
E: Ketopantoate hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,94810
Polymers146,8265
Non-polymers1225
Water1,892105
1
A: Ketopantoate hydroxymethyltransferase
B: Ketopantoate hydroxymethyltransferase
C: Ketopantoate hydroxymethyltransferase
D: Ketopantoate hydroxymethyltransferase
E: Ketopantoate hydroxymethyltransferase
hetero molecules

A: Ketopantoate hydroxymethyltransferase
B: Ketopantoate hydroxymethyltransferase
C: Ketopantoate hydroxymethyltransferase
D: Ketopantoate hydroxymethyltransferase
E: Ketopantoate hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,89620
Polymers293,65310
Non-polymers24310
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
MethodPQS
2
C: Ketopantoate hydroxymethyltransferase
hetero molecules

E: Ketopantoate hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7794
Polymers58,7312
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area5640 Å2
ΔGint-53 kcal/mol
Surface area19040 Å2
MethodPISA
3
A: Ketopantoate hydroxymethyltransferase
hetero molecules

D: Ketopantoate hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7794
Polymers58,7312
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area5600 Å2
ΔGint-53 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.8, 106.8, 224.4
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein
Ketopantoate hydroxymethyltransferase / E.C.2.1.2.11 / 3-methyl-2-oxobutanoate hydroxymethyltransferase / panB


Mass: 29365.287 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: PANB / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5Q8, UniProt: P9WIL7*PLUS, 3-methyl-2-oxobutanoate hydroxymethyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.85 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Magnesium formate, ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
2200 mMmagnesium formate1reservoir
310 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 36560 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 72.5 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.5
Reflection shellResolution: 2.8→2.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.9
Reflection
*PLUS
Highest resolution: 2.8 Å / % possible obs: 97.8 %
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 99.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
CNS1.1refinement
DMphasing
RefinementMethod to determine structure: SAS with averaging / Resolution: 2.8→92.53 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1874 5.1 %RANDOM
Rwork0.239 ---
obs-36534 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.469 Å2 / ksol: 0.348838 e/Å3
Displacement parametersBiso mean: 48.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å23.56 Å20 Å2
2--1.65 Å20 Å2
3----3.29 Å2
Refine analyzeLuzzati coordinate error free: 0.47 Å / Luzzati sigma a free: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.8→92.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9135 0 5 105 9245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.74
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 334 5.5 %
Rwork0.318 5731 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Lowest resolution: 2.85 Å / Rfactor Rfree: 0.342 / Rfactor Rwork: 0.313

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