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

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Basic information

Entry
Database: PDB / ID: 4cyu
TitleStaphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophosphokinase in complex with AMPCPP
Components(7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN- ...) x 2
KeywordsTRANSFERASE / S.AUREUS / 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 / :
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 15, 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_alt_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_alt_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.pdbx_ptnr2_label_alt_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_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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
C: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
D: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,67518
Polymers73,2154
Non-polymers2,46014
Water23413
1
A: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9795
Polymers18,3031
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9805
Polymers18,3041
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8584
Polymers18,3041
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8584
Polymers18,3041
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.002, 94.263, 62.989
Angle α, β, γ (deg.)90.00, 112.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN- ... , 2 types, 4 molecules ABCD

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


Mass: 18303.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C8MLE4, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Protein 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE / HPPK


Mass: 18304.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / 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 , 4 types, 27 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 2.39 Å3/Da / Density % sol: 48.62 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PROTEIN 6.9 MG/ML 1 MM AMPCPP, 2 MM MAGNESIUM CHLORIDE, MAGNESIUM ACETATE 0.119 M, PEG8000 12.6% W/V, TRIS CHLORIDE 0.12 M, SITTING DROP, 281 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.008
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.7→45.53 Å / Num. obs: 18506 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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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: 2.7→45.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY RESIDUES OF LOOP 2 ARE NOT MODELLED IN CHAINS A (RESIDUES 45-48) AND B (RESIDUES 46-48) DUE TO POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24223 838 4.5 %RANDOM
Rwork0.19217 ---
obs0.19433 17651 99.96 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.203 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å22.65 Å2
2--0.06 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 148 13 5160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195293
X-RAY DIFFRACTIONr_bond_other_d00.025116
X-RAY DIFFRACTIONr_angle_refined_deg1.4932.047224
X-RAY DIFFRACTIONr_angle_other_deg3.437311796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3045619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79124.807233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63515943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6551536
X-RAY DIFFRACTIONr_chiral_restr0.0710.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215702
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021094
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 55 -
Rwork0.319 1303 -
obs--100 %

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