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- PDB-3ez4: Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransfe... -

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Basic information

Entry
Database: PDB / ID: 3ez4
TitleCrystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei
Components3-methyl-2-oxobutanoate hydroxymethyltransferase
KeywordsTRANSFERASE / Cytoplasm / Magnesium / Metal-binding / Methyltransferase / Pantothenate biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


3-methyl-2-oxobutanoate hydroxymethyltransferase / 3-methyl-2-oxobutanoate hydroxymethyltransferase activity / pantothenate biosynthetic process / magnesium ion binding / 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 speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei
Authors: Edwards, T.E.
History
DepositionOct 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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_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: 3-methyl-2-oxobutanoate hydroxymethyltransferase
B: 3-methyl-2-oxobutanoate hydroxymethyltransferase
C: 3-methyl-2-oxobutanoate hydroxymethyltransferase
D: 3-methyl-2-oxobutanoate hydroxymethyltransferase
E: 3-methyl-2-oxobutanoate hydroxymethyltransferase
F: 3-methyl-2-oxobutanoate hydroxymethyltransferase
G: 3-methyl-2-oxobutanoate hydroxymethyltransferase
H: 3-methyl-2-oxobutanoate hydroxymethyltransferase
I: 3-methyl-2-oxobutanoate hydroxymethyltransferase
J: 3-methyl-2-oxobutanoate hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,03915
Polymers285,42810
Non-polymers6115
Water26,0681447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21860 Å2
ΔGint-114 kcal/mol
Surface area84260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.784, 187.556, 83.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
3-methyl-2-oxobutanoate hydroxymethyltransferase / Ketopantoate hydroxymethyltransferase / KPHMT


Mass: 28542.816 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: 721, 76, 808, BPSL2824, panB / Plasmid: BG1861 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63R49, UniProt: Q3JP15*PLUS, 3-methyl-2-oxobutanoate hydroxymethyltransferase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1447 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PACT screen condition H11, 0.1 M BisTris propane, 20% PEG 3350, 0.2 M Na Citrate, 0.4/0.4 uL drops, 24.4 mg/mL protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorDate: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 157415 / % possible obs: 98.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.107 / Χ2: 0.924 / Net I/σ(I): 13.461
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.3 / Num. unique all: 15125 / Χ2: 0.483 / % possible all: 96

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1M3U

1m3u


Resolution: 2.1→38.55 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.831 / SU B: 4.585 / SU ML: 0.121 / SU R Cruickshank DPI: 0.218 / SU Rfree: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 7886 5 %RANDOM
Rwork0.195 ---
obs0.197 157130 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.39 Å2 / Biso mean: 23.973 Å2 / Biso min: 5.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17895 0 40 1447 19382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02218242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211954
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.97324814
X-RAY DIFFRACTIONr_angle_other_deg1.028329222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.63852412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30423.701708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.926152816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.16215126
X-RAY DIFFRACTIONr_chiral_restr0.1030.22941
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023579
X-RAY DIFFRACTIONr_mcbond_it0.9771.512074
X-RAY DIFFRACTIONr_mcbond_other0.2541.54946
X-RAY DIFFRACTIONr_mcangle_it1.802219238
X-RAY DIFFRACTIONr_scbond_it3.02836168
X-RAY DIFFRACTIONr_scangle_it5.0354.55576
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 538 -
Rwork0.201 10458 -
all-10996 -
obs--94.62 %

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