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- PDB-1ex8: CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPH... -

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Basic information

Entry
Database: PDB / ID: 1ex8
TitleCRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE COMPLEXED WITH HP4A, THE TWO-SUBSTRATE-MIMICKING INHIBITOR
Components6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
KeywordsTRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / PTERIN / ATP / BISUBSTRATE-MIMICKING INHIBITOR / ANTIMICROBIAL AGENT / DRUG DESIGN / SUBSTRATE SPECIFICITY / ACTIVE-SITE ARCHITECTURE
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 / magnesium ion binding / ATP 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-A4P / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBlaszczyk, J. / Ji, X.
Citation
Journal: J.Med.Chem. / Year: 2001
Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies.
Authors: Shi, G. / Blaszczyk, J. / Ji, X. / Yan, H.
#1: Journal: Structure / Year: 1999
Title: Crystal Structure of 6-hydroxymethyl-7,8-dihydropterin Pyrophosphokinase, a Potential Target for the Development of Novel Antimicrobial Agents
Authors: Xiao, B. / Shi, G. / Chen, X. / Yan, H. / Ji, X.
History
DepositionMay 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / 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_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.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.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7914
Polymers17,9671
Non-polymers8243
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.053, 61.857, 67.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE


Mass: 17966.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-A4P / 6-(ADENOSINE TETRAPHOSPHATE-METHYL)-7,8-DIHYDROPTERIN


Mass: 764.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24N10O17P4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.13 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, magnesium chloride, Tris-HCl, glycerol, acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
235 mMHP4A1drop
350 mM1dropMgCl2
410 MTris-HCl1drop
528 %(w/v)PEG40001reservoir
60.18 Mammonium acetate1reservoir
70.15 Msodium acetate1reservoir
810 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 1999 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 14188 / Num. obs: 12732 / % possible obs: 89.5 % / Observed criterion σ(F): 0.025 / Observed criterion σ(I): 0.05 / Redundancy: 3.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 5.9
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.056 / Num. unique all: 1384 / % possible all: 77.6
Reflection shell
*PLUS
% possible obs: 77.6 %

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EQO

1eqo
PDB Unreleased entry


Resolution: 1.85→40 Å / Num. parameters: 5668 / Num. restraintsaints: 5447 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
Details: Least-squares refinement using the Konnert-Hendrickson conjugate-gradient algorithm
RfactorNum. reflection% reflectionSelection details
Rfree0.242 614 -RANDOM
Rwork0.2029 ---
obs0.1854 9368 85.4 %-
all-12025 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1478
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 50 167 1484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.081
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.212 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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