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- PDB-3mcm: Crystal Structure of the 6-hyroxymethyl-7,8-dihydropterin pyropho... -

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Basic information

Entry
Database: PDB / ID: 3mcm
TitleCrystal Structure of the 6-hyroxymethyl-7,8-dihydropterin pyrophosphokinase dihydropteroate synthase bifunctional enzyme from Francisella tularensis
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
KeywordsTRANSFERASE / folate / TIM barrel / kinase / synthase / HPPK / DHPS / pterin
Function / homology7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / Dihydropteroate synthase-like / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesFrancisella tularensis subsp. holarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPemble IV, C.W. / Mehta, P.K. / Mehra, S. / Li, Z. / Lee, R.E. / White, S.W.
CitationJournal: Plos One / Year: 2010
Title: Crystal structure of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.dihydropteroate synthase bifunctional enzyme from Francisella tularensis.
Authors: Pemble, C.W. / Mehta, P.K. / Mehra, S. / Li, Z. / Nourse, A. / Lee, R.E. / White, S.W.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
B: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1993
Polymers101,1752
Non-polymers241
Water2,378132
1
A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6122
Polymers50,5871
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)50,5871
Polymers50,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.821, 57.779, 105.127
Angle α, β, γ (deg.)91.130, 99.390, 111.640
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase


Mass: 50587.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. holarctica (bacteria)
Strain: LVS / Gene: folP/K, FTL_1265 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2A2W3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: TRIS, Na Acetate, PEG 4000, Glyerol, pH 8.0, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→38.6 Å / Num. all: 46769 / Num. obs: 44140 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 23.6
Reflection shellResolution: 2.2→2.278 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.3 / Num. unique all: 3743 / % possible all: 80.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2QX0, 1TWW

2qx0

1tww


Resolution: 2.2→38.442 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.96 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2225 5.05 %random
Rwork0.215 ---
obs0.219 44083 94.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.399 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 101.79 Å2 / Biso mean: 41.898 Å2 / Biso min: 13.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.478 Å20.081 Å20.273 Å2
2---0.317 Å2-0.422 Å2
3---0.795 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 1 132 6154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086119
X-RAY DIFFRACTIONf_angle_d1.1278231
X-RAY DIFFRACTIONf_chiral_restr0.076978
X-RAY DIFFRACTIONf_plane_restr0.0041027
X-RAY DIFFRACTIONf_dihedral_angle_d19.3172339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2780.3031690.2373530369979
2.278-2.3690.3422010.2373790399185
2.369-2.4770.3042370.244019425691
2.477-2.6070.3231980.2254269446795
2.607-2.770.3162550.2414318457398
2.77-2.9840.2952040.2314386459098
2.984-3.2840.292530.2174364461799
3.284-3.7590.2672440.2014367461199
3.759-4.7350.2342330.1884415464899
4.735-38.4480.262310.2114400463199

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