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- PDB-1kbr: CRYSTAL STRUCTURE OF UNLIGATED HPPK(R92A) FROM E.COLI AT 1.55 ANG... -

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Basic information

Entry
Database: PDB / ID: 1kbr
TitleCRYSTAL STRUCTURE OF UNLIGATED HPPK(R92A) FROM E.COLI AT 1.55 ANGSTROM RESOLUTION
Components6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
KeywordsTRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / PTERIN / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN / 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
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBlaszczyk, J. / Ji, X.
Citation
Journal: Biochemistry / Year: 2003
Title: Dynamic Roles of Arginine Residues 82 and 92 of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase: Crystallographic Studies
Authors: Blaszczyk, J. / Li, Y. / 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.
#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.
#4: Journal: J.Biol.Chem. / Year: 2001
Title: Unusual Conformational Changes in 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Revealed by X-Ray Crystallography and NMR
Authors: Xiao, B. / Shi, G. / Gao, J. / Blaszczyk, J. / Liu, Q. / Ji, X. / Yan, H.
History
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Aug 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)17,9162
Polymers17,8801
Non-polymers351
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.340, 46.943, 42.907
Angle α, β, γ (deg.)90.00, 110.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE / 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE / HPPK


Mass: 17880.418 Da / Num. of mol.: 1 / Mutation: R92A
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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 meas: 35 Mg/m3 / Density % sol: 35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, SODIUM CHLORIDE, ACETATE , pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal grow
*PLUS
Temperature: 18-20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
330 %(w/v)PEG40001reservoir
4200 mMsodium acetate1reservoir
5100 mM1reservoirNaCl
6100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97125 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2001 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971251
20.979461
ReflectionResolution: 1.55→30 Å / Num. all: 19262 / Num. obs: 19262 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.246 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.5882
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.012 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8248 / Num. unique all: 1843 / % possible all: 92.5
Reflection
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 30 Å / Num. measured all: 81783
Reflection shell
*PLUS
% possible obs: 92.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1IM6

1im6


Resolution: 1.55→30 Å / Num. parameters: 5140 / Num. restraintsaints: 5338 / Isotropic thermal model: ISOTROPIC / 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
Rfree0.208 944 5.213 %RANDOM
Rwork0.168 ---
all0.192 18109 --
obs0.16 13591 91.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1975) 201-228
Displacement parametersBiso mean: 23.307 Å2
Refine analyzeLuzzati coordinate error obs: 0.155 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 4 / Occupancy sum hydrogen: 1170 / Occupancy sum non hydrogen: 1491
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 0 1 230 1508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0.054
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.55-1.660.226X-RAY DIFFRACTION18619
1.66-1.760.206X-RAY DIFFRACTION18749
1.76-1.870.19X-RAY DIFFRACTION17059
1.87-2.020.178X-RAY DIFFRACTION18009
2.02-2.20.17X-RAY DIFFRACTION18259
2.2-2.480.152X-RAY DIFFRACTION18189
2.48-2.960.144X-RAY DIFFRACTION18309
2.96-4.240.139X-RAY DIFFRACTION17719
4.24-300.205X-RAY DIFFRACTION9049
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.027
X-RAY DIFFRACTIONs_chiral_restr0.049

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