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- PDB-3hsd: Crystal structure of E. coli HPPK(Y53A) -

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Basic information

Entry
Database: PDB / ID: 3hsd
TitleCrystal structure of E. coli HPPK(Y53A)
ComponentsHPPK2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
KeywordsTRANSFERASE / alpha beta / ATP-binding / Folate biosynthesis / Kinase / Nucleotide-binding
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 / phosphorylation / 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 / molecular replacement / Resolution: 1.652 Å
AuthorsBlaszczyk, J. / Li, Y. / Yan, H. / Ji, X.
Citation
Journal: To be Published
Title: Pterin-binding site mutation Y53A, N55A or F123A and activity of E. coli HPPK.
Authors: Li, Y. / 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
DepositionJun 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Sep 6, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HPPK
B: HPPK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,43715
Polymers35,7492
Non-polymers68813
Water7,476415
1
A: HPPK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2959
Polymers17,8741
Non-polymers4208
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HPPK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1436
Polymers17,8741
Non-polymers2685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.04, 47.47, 72.53
Angle α, β, γ (deg.)90.00, 108.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17874.438 Da / Num. of mol.: 2 / Mutation: Y54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K 12 / Gene: b0142, foIK, folK, JW0138 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / 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.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Sodium acetate, Magnesium chloride, Glycerol, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2000 / Details: mirrors
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→34.31 Å / Num. all: 32113 / Num. obs: 32113 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.004 / Net I/σ(I): 13.623
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2 / Num. unique all: 3214 / Χ2: 1.009 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G4C

1g4c


Resolution: 1.652→20.608 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
Details: THE STRUCTURE WAS REFINED FOR A TOTAL OF 28 CYCLES, INCLUDING 7 CYCLES WITH CNS, 8 CYCLES WITH SHELX, AND 13 CYCLES WITH PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1000 3.12 %Random
Rwork0.16 ---
all0.162 32092 --
obs0.162 32092 98.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.922 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso max: 55.86 Å2 / Biso mean: 15.279 Å2 / Biso min: 4.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.898 Å2-0 Å22.572 Å2
2---0.33 Å20 Å2
3----0.569 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.652→20.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 38 415 2973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052697
X-RAY DIFFRACTIONf_angle_d1.0113669
X-RAY DIFFRACTIONf_chiral_restr0.073407
X-RAY DIFFRACTIONf_plane_restr0.005481
X-RAY DIFFRACTIONf_dihedral_angle_d16.4621024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.652-1.7390.2541440.20544114555448598
1.739-1.8480.291420.189445045924589100
1.848-1.990.2561450.17451246574610100
1.99-2.1910.2031470.15444574604460499
2.191-2.5070.2331430.15144674610465799
2.507-3.1570.2121420.15544474589459298
3.157-20.610.1641370.14343484485455594

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