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- PDB-3hsg: Crystal structure of E. coli HPPK(Y53A) in complex with MgAMPCPP -

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Basic information

Entry
Database: PDB / ID: 3hsg
TitleCrystal structure of E. coli HPPK(Y53A) in complex with MgAMPCPP
ComponentsHPPK
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
ACETATE ION / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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: 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
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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7669
Polymers17,8741
Non-polymers8928
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.94, 48.02, 74.20
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HPPK / 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.: 1 / 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

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Non-polymers , 6 types, 220 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 1.79 Å3/Da / Density % sol: 31.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, Ammonium acetate, Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 1999 / Details: mirrors
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.14→37.1 Å / Num. all: 46812 / Num. obs: 46812 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.016 / Net I/σ(I): 19.386
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2296 / Χ2: 1.028 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q0N

1q0n


Resolution: 1.14→32.348 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.877 / SU ML: 0.12
Isotropic thermal model: Anisotropic B factors for non-H atoms of full occupancy
Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
Details: THE STRUCTURE WAS REFINED FOR A TOTAL OF 40 CYCLES, INCLUDING 3 CYCLES WITH CNS, 15 CYCLES WITH SHELX, AND 22 CYCLES WITH PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1000 2.14 %Random
Rwork0.147 ---
all0.147 46746 --
obs0.147 46746 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.89 Å2 / ksol: 0.414 e/Å3
Displacement parametersBiso max: 49.82 Å2 / Biso mean: 14.369 Å2 / Biso min: 3.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.541 Å2-0 Å20 Å2
2---0.864 Å2-0 Å2
3---0.322 Å2
Refinement stepCycle: LAST / Resolution: 1.14→32.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 54 212 1526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061482
X-RAY DIFFRACTIONf_angle_d1.1192033
X-RAY DIFFRACTIONf_chiral_restr0.075221
X-RAY DIFFRACTIONf_plane_restr0.006269
X-RAY DIFFRACTIONf_dihedral_angle_d14.428593
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 (%)
1.14-1.1990.2931390.24663676506650697
1.199-1.2750.2411380.20163246462646297
1.275-1.3730.2031410.1664216562656297
1.373-1.5110.1821400.13864206560656097
1.511-1.730.1611440.11765696713671399
1.73-2.180.1641460.116669968456845100
2.18-32.3610.1511520.141694670987098100

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