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- PDB-1ru2: CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E.COLI HPPK(V83G/DEL84-... -

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Basic information

Entry
Database: PDB / ID: 1ru2
TitleCRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E.COLI HPPK(V83G/DEL84-89) WITH MGAMPCPP AND 6-HYDROXYMETHYLPTERIN AT 1.48 ANGSTROM RESOLUTION (ORTHORHOMBIC FORM)
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / 6-HYDROXYMETHYLPTERIN / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN / ANTIMICROBIAL AGENT / DRUG DESIGN / DELETION MUTANT
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 6-HYDROXYMETHYLPTERIN / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsBlaszczyk, J. / Ji, X.
Citation
Journal: Biochemistry / Year: 2004
Title: Essential Roles of a Dynamic Loop in the Catalysis of 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase.
Authors: Blaszczyk, J. / Li, Y. / Wu, Y. / Shi, G. / 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.
#2: Journal: Structure / Year: 2000
Title: Catalytic Center Assembly of Hppk as Revealed by the Crystal Structure of a Ternary Complex at 1.25 A Resolution
Authors: Blaszczyk, J. / Shi, G. / Yan, H. / Ji, X.
#3: 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.
History
DepositionDec 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 21, 2016Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Aug 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,8776
Polymers17,0941
Non-polymers7825
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.609, 63.156, 36.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21A-330-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase / 7 / 8-dihydro-6-hydroxymethylpterin-pyrophosphokinase / HPPK / 6-hydroxymethyl-7 / 8-dihydropterin ...7 / 8-dihydro-6-hydroxymethylpterin-pyrophosphokinase / HPPK / 6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK


Mass: 17094.482 Da / Num. of mol.: 1 / Mutation: V83G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FOLK, B0142 / 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

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Non-polymers , 5 types, 135 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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-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
#5: Chemical ChemComp-HHR / 6-HYDROXYMETHYLPTERIN


Mass: 193.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N5O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.73 Å3/Da / Density % sol: 28.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, MAGNESIUM CHLORIDE, ACETATE, GLYCEROL, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19 mg/mlprotein1drop
215 mMHP1drop
350 mM1dropMgCl2
40.1 MTris-HCl1droppH8.
530 %(w/v)PEG40001reservoir
60.2 Mammonium acetate1reservoir
71 %(v/v)glycerol1reservoir
80.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.00928 / Wavelength: 1.00928 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2001 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00928 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 20535 / Num. obs: 20535 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.414 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 14.6166
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 6.31 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.884 / Num. unique all: 1993 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.48 Å / Num. measured all: 152250
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1Q0N

1q0n


Resolution: 1.48→30 Å / Num. parameters: 11342 / Num. restraintsaints: 14982 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: FULL MATRIX LEAST-SQUARES PROCEDURE, WITH BLOCK OF PARAMETERS SET FOR EACH CYCLE OF ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1015 5.25 %RANDOM
Rwork0.164 ---
all0.172 19335 --
obs0.158 15068 94.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1975) 201-228
Displacement parametersBiso mean: 29.553 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 2 / Occupancy sum hydrogen: 1106 / Occupancy sum non hydrogen: 1336.5
Refinement stepCycle: LAST / Resolution: 1.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 48 130 1338
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.099
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps0.08
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.48-1.560.245X-RAY DIFFRACTION19529
1.56-1.650.209X-RAY DIFFRACTION19879
1.65-1.750.186X-RAY DIFFRACTION19249
1.75-1.870.167X-RAY DIFFRACTION19029
1.87-2.020.147X-RAY DIFFRACTION19329
2.02-2.230.137X-RAY DIFFRACTION19559
2.23-2.560.135X-RAY DIFFRACTION19229
2.56-3.250.139X-RAY DIFFRACTION19059
3.25-300.176X-RAY DIFFRACTION19099
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.027
X-RAY DIFFRACTIONs_chiral_restr0.045

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