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- PDB-3hcx: Crystal structure of E. coli HPPK(N10A) -

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Basic information

Entry
Database: PDB / ID: 3hcx
TitleCrystal structure of E. coli HPPK(N10A)
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
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 / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsBlaszczyk, J. / Li, Y. / Yan, H. / Ji, X.
Citation
Journal: To be Published
Title: Role of loop coupling in enzymatic catalysis and conformational dynamics
Authors: Blaszczyk, J. / Li, Y. / 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
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 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 / 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 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: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0813
Polymers17,9241
Non-polymers1582
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.33, 51.74, 41.39
Angle α, β, γ (deg.)90.00, 109.38, 90.00
Int Tables number4
Space group name H-MP1211

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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: 17923.510 Da / Num. of mol.: 1 / Mutation: N10A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Sodium acetate, 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: 0.917 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 1999 / Details: mirrors
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 14669 / Num. obs: 14669 / % possible obs: 99.8 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.047 / Χ2: 1 / Net I/σ(I): 24.571
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.92 / Num. unique all: 1471 / Χ2: 0.997 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1HKA

1hka


Resolution: 1.75→19.524 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.846 / SU ML: 0.27 / 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 24 cycles, including 8 cycles with CNS, 7 cycles with SHELX, and 9 cycles with PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1000 6.82 %Random
Rwork0.184 ---
obs0.186 14654 99.78 %-
all-14654 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.825 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 62.68 Å2 / Biso mean: 29.043 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.626 Å2-0 Å21.837 Å2
2---3.605 Å2-0 Å2
3---2.979 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 9 169 1442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071366
X-RAY DIFFRACTIONf_angle_d1.0541865
X-RAY DIFFRACTIONf_chiral_restr0.075208
X-RAY DIFFRACTIONf_plane_restr0.005245
X-RAY DIFFRACTIONf_dihedral_angle_d18.148510
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 (%)
1.75-1.8430.2851400.252191820582058100
1.843-1.9580.2661430.218195620992099100
1.958-2.1090.2851410.196192420652065100
2.109-2.3210.2091440.181195220962096100
2.321-2.6560.2491430.186196121042104100
2.656-3.3440.241440.18195921032103100
3.344-19.5250.171450.16819842129212999

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