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- PDB-5ets: S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase com... -

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Basic information

Entry
Database: PDB / ID: 5ets
TitleS. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.95 angstrom resolution
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE/TRANSFERASE inhibitor / inhibitor / complex / ampcpp / pyrophosphokinase / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / ATP binding / metal ion binding
Similarity search - Function
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5RX / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDennis, M.L. / Peat, T.S. / Swarbrick, J.D.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli.
Authors: Dennis, M.L. / Pitcher, N.P. / Lee, M.D. / DeBono, A.J. / Wang, Z.C. / Harjani, J.R. / Rahmani, R. / Cleary, B. / Peat, T.S. / Baell, J.B. / Swarbrick, J.D.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,40013
Polymers36,6082
Non-polymers1,79211
Water2,774154
1
B: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2127
Polymers18,3041
Non-polymers9086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1896
Polymers18,3041
Non-polymers8855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.790, 68.580, 52.990
Angle α, β, γ (deg.)90.00, 105.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 18304.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: RK60_02090, RK67_01645, RK72_06915, RK74_04210, RK75_00240, RK80_01970, RK83_05435, RK84_03130, RK95_04415, RK96_04825, RK98_03440, RK99_07885, RL05_10010, RL06_09555, RL08_05305, TM59_02255
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H1ZSM1, UniProt: Q2G0Q5*PLUS, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase

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Non-polymers , 5 types, 165 molecules

#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-5RX / 2-azanyl-8-[(4-chlorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one


Mass: 307.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10ClN5OS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: Protein 6.9 mg/mL 1 mM AMPCPP, 1 mM inhibitor, 0.182 MgCl2, 0.1 M tris chloride, 17.2%w/v PEG8000, 50 mM sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0329 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0329 Å / Relative weight: 1
ReflectionResolution: 1.95→40.9 Å / Num. obs: 24055 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 10
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ETQ

5etq


Resolution: 1.95→40.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21815 1228 5.1 %RANDOM
Rwork0.18898 ---
obs0.19046 22747 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.637 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0.6 Å2
2--1.47 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 109 154 2769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192658
X-RAY DIFFRACTIONr_bond_other_d00.022536
X-RAY DIFFRACTIONr_angle_refined_deg1.7472.043624
X-RAY DIFFRACTIONr_angle_other_deg3.56935840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30624.828116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23815470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4221518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212986
X-RAY DIFFRACTIONr_gen_planes_other0.010.02548
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_it0.8640.8781254
X-RAY DIFFRACTIONr_mcbond_other0.8520.8771253
X-RAY DIFFRACTIONr_mcangle_it1.3461.3081564
X-RAY DIFFRACTIONr_mcangle_other1.3511.3091565
X-RAY DIFFRACTIONr_scbond_it1.7181.1251404
X-RAY DIFFRACTIONr_scbond_other1.7171.1251405
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6231.6072061
X-RAY DIFFRACTIONr_long_range_B_refined4.2118.0583106
X-RAY DIFFRACTIONr_long_range_B_other4.2118.063107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 90 -
Rwork0.262 1665 -
obs--98.98 %

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