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- PDB-4cwb: Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophos... -

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Basic information

Entry
Database: PDB / ID: 4cwb
TitleStaphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophosphokinase in complex with AMPCPP and an inhibitor
Components7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
KeywordsTRANSFERASE / FOLATE / STRUCTURE-BASED DRUG DESIGN
Function / homology7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / NITRATE ION / Chem-X6L / :
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsDennis, M.L. / Swarbrick, J.D. / Peat, T.S.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives as Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase ...Title: Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives as Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase from Staphylococcus Aureus.
Authors: Dennis, M.L. / Chhabra, S. / Wang, Z. / Debono, A. / Dolezal, O. / Newman, J. / Pitcher, N.P. / Rahmani, R. / Cleary, B. / Barlow, N. / Hattarki, M. / Graham, B. / Peat, T.S. / Baell, J.B. / Swarbrick, J.D.
History
DepositionApr 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2976
Polymers18,3041
Non-polymers9935
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.817, 83.817, 52.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE / HPPK


Mass: 18304.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C8MLE4, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-X6L / 2-amino-8-[2-oxo-2-(4-phenylphenyl)ethyl]sulfanyl-1,9-dihydropurin-6-one


Mass: 377.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15N5O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsHEXAHISTIDINE-TAG WITH THROMBIN CLEAVAGE AT THE N-TERMINUS

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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: 2.93 Å3/Da / Density % sol: 58.1 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PROTEIN 6.9 MG/ML 1 MM AMPCPP, 1 MM INHIBITOR, 2 MM MAGNESIUM CHLORIDE, AMMONIUM NITRATE 0.275 M, PEG3350 22.2% W/V, SITTING DROP, 281 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.56→42.29 Å / Num. obs: 29793 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 1.56→1.58 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.7 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AD6

4ad6


Resolution: 1.56→42.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.162 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. AN ALTERNATE CONFORMATION OF THE LOOP 3 RESIDUE LYS86 IS SUGGESTED, THIS WAS NOT MODELLED DUE TO POOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. AN ALTERNATE CONFORMATION OF THE LOOP 3 RESIDUE LYS86 IS SUGGESTED, THIS WAS NOT MODELLED DUE TO POOR DENSITY. THE TERMINAL RESIDUE LYS158 IS SUGGESTED TO ADOPT MULTIPLE CONFORMATIONS. ONLY THE PREDOMINANT CONFORMATION IS MODELLED DUE TO ELSEWISE POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.17816 1505 5.1 %RANDOM
Rwork0.15877 ---
obs0.15972 28270 99.68 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.534 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.24 Å20 Å2
2--0.24 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.56→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 64 141 1478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191466
X-RAY DIFFRACTIONr_bond_other_d0.0010.021398
X-RAY DIFFRACTIONr_angle_refined_deg1.62.0392012
X-RAY DIFFRACTIONr_angle_other_deg0.77133239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56225.23165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55315267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.576159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211714
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02324
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.558→1.599 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 115 -
Rwork0.216 2013 -
obs--97.84 %

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