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- PDB-1rb0: CRYSTAL STRUCTURE OF A BINARY COMPLEX OF E. COLI HPPK WITH 6-HYDR... -

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Basic information

Entry
Database: PDB / ID: 1rb0
TitleCRYSTAL STRUCTURE OF A BINARY COMPLEX OF E. COLI HPPK WITH 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE AT 1.35 ANGSTROM RESOLUTION
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / CATALYTIC MECHANISM / FOLATE / HPPK / PTERIN / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN / 6-HYDROXYMETHYLPTERIN / TERNARY COMPLEX / BINARY COMPLEX / SUBSTRATE SPECIFICITY / PRODUCT RELEASE / 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
6-HYDROXYMETHYLPTERIN-DIPHOSPHATE / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBlaszczyk, J. / Ji, X.
Citation
Journal: Structure / Year: 2004
Title: Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Authors: Blaszczyk, J. / Shi, G. / Li, Y. / 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.
#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.
History
DepositionOct 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3202
Polymers17,9671
Non-polymers3531
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.591, 67.519, 35.165
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-89-

TRP

21A-298-

HOH

31A-479-

HOH

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Components

#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, 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
#2: Chemical ChemComp-HH2 / 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE / [PTERIN-6-YL METHANYL]-PHOSPHONOPHOSPHATE


Mass: 353.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O8P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 1.96 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, ACETATE, SODIUM AZIDE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97793 / Wavelength: 0.97793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2000 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 27560 / Num. obs: 27560 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.79 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.4146
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.423 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.252 / Num. unique all: 2664 / % possible all: 98.4

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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: 1.35→30 Å / Num. parameters: 12488 / Num. restraintsaints: 16542 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: LEAST-SQUARES ANISOTROPIC REFINEMENT USING THE KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1297 4.946 %RANDOM
Rwork0.1374 ---
all-26223 --
obs-20385 94.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975) 201-228
Displacement parametersBiso mean: 15.599 Å2
Refine analyzeLuzzati coordinate error obs: 0.161 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 16 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1581
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 22 298 1636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.042
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.157
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.057
X-RAY DIFFRACTIONs_approx_iso_adps0.077
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.35-1.420.204X-RAY DIFFRACTION27419
1.42-1.50.175X-RAY DIFFRACTION25129
1.5-1.60.15X-RAY DIFFRACTION26429
1.6-1.720.135X-RAY DIFFRACTION26779
1.72-1.870.123X-RAY DIFFRACTION25809
1.87-2.070.118X-RAY DIFFRACTION25879
2.07-2.430.11X-RAY DIFFRACTION26339
2.43-3.230.117X-RAY DIFFRACTION26019
3.23-300.159X-RAY DIFFRACTION20599

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