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- PDB-1q0n: CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIH... -

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Basic information

Entry
Database: PDB / ID: 1q0n
TitleCRYSTAL STRUCTURE OF A TERNARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE FROM E. COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 1.25 ANGSTROM RESOLUTION
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / PTERIN / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN / TERNARY COMPLEX / SUBSTRATE SPECIFICITY / ANTIMICROBIAL AGENT / DRUG DESIGN
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
ACETATE ION / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Chem-PH2 / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBlaszczyk, J. / Ji, X.
Citation
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.
#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
DepositionJul 16, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 26, 2003ID: 1eqo
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

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)18,98710
Polymers17,9671
Non-polymers1,0219
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.591, 37.743, 57.909
Angle α, β, γ (deg.)90.00, 116.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-167-

ACT

21A-167-

ACT

31A-406-

HOH

41A-414-

HOH

51A-472-

HOH

61A-538-

HOH

71A-539-

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: 17966.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FOLK OR 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 , 6 types, 348 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: 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
#6: Chemical ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.04 Å3/Da / Density % sol: 35.7 %
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/mlHPPK1drop
225 mMHP1drop
315 mMAMPCPP1drop
450 mM1dropMgCl2
510 mMTris-HCl1droppH8.0
630 %(w/v)PEG40001reservoir
70.2 Mammonium acetate1reservoir
80.1 Msodium acetate1reservoirpH4.6
92 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 1999 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 38972 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.8
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.156 / Num. unique all: 3769 / % possible all: 97.1
Reflection
*PLUS
Num. measured all: 131959
Reflection shell
*PLUS
% possible obs: 97.1 % / Mean I/σ(I) obs: 2.2

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Processing

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

1hka


Resolution: 1.25→30 Å / Num. parameters: 14405 / Num. restraintsaints: 17565 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
Details: FULL-MATRIX LEAST-SQUARES PROCEDURE, WITH BLOCK OF PARAMETERS SET FOR EACH CYCLE OF ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.147 1894 5.114 %RANDOM
Rwork0.101 ---
all0.115 38972 --
obs0.096 37078 94.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201- 202
Displacement parametersBiso mean: 14.67 Å2
Refine analyzeLuzzati coordinate error free: 0.12 Å / Num. disordered residues: 10 / Occupancy sum hydrogen: 1296 / Occupancy sum non hydrogen: 1664
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 72 343 1711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.157
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.167
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.225
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.019
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.087
LS refinement shell
Resolution (Å)Rfactor RworkRefine-ID
1.25-1.320.161X-RAY DIFFRACTION
1.32-1.390.129X-RAY DIFFRACTION
1.39-1.460.113X-RAY DIFFRACTION
1.46-1.560.096X-RAY DIFFRACTION
1.56-1.690.086X-RAY DIFFRACTION
1.69-1.860.082X-RAY DIFFRACTION
1.86-2.120.086X-RAY DIFFRACTION
2.12-2.650.082X-RAY DIFFRACTION
2.65-7.040.105X-RAY DIFFRACTION
7.04-300.259X-RAY DIFFRACTION
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.131 / Rfactor Rwork: 0.095
Solvent computation
*PLUS
Displacement parameters
*PLUS

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