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- PDB-3ip0: Crystal structure of E. coli HPPK in complex with MgAMPCPP and 6-... -

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Basic information

Entry
Database: PDB / ID: 3ip0
TitleCrystal structure of E. coli HPPK in complex with MgAMPCPP and 6-hydroxymethylpterin/6-carboxypterin
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
ACETATE ION / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 6-HYDROXYMETHYLPTERIN / 6-CARBOXYPTERIN / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.89 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-dihydroptein pyrophosphokinase: Crystallographic studies
Authors: Blaszczyk, J. / Li, Y. / Shi, G. / Yan, H. / Ji, X.
#1: Journal: Structure / Year: 2000
Title: Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25-angstrom resolution
Authors: Blaszczyk, J. / Shi, G. / Yan, H. / Ji, X.
History
DepositionAug 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
SupersessionOct 27, 2009ID: 3H4A
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2016Group: Advisory
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)19,26313
Polymers17,9671
Non-polymers1,29712
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules

A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,52626
Polymers35,9332
Non-polymers2,59324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6080 Å2
ΔGint-92 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.470, 37.910, 57.850
Angle α, β, γ (deg.)90.00, 117.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-192-

CL

21A-193-

CL

31A-450-

HOH

41A-451-

HOH

51A-452-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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) / 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 , 7 types, 337 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-HHR / 6-HYDROXYMETHYLPTERIN


Mass: 193.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N5O2
#5: Chemical ChemComp-HHS / 6-CARBOXYPTERIN / 2-amino-4-oxo-3,4-dihydropteridine-6-carboxylic acid


Mass: 207.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5N5O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, Ammonium acetate, Sodium acetate, Glycerol., 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: 1.00928 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: 1.00928 Å / Relative weight: 1
ReflectionResolution: 0.89→40 Å / Num. all: 100866 / Num. obs: 100866 / % possible obs: 93.1 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 4.44 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.003 / Net I/σ(I): 14.5
Reflection shellResolution: 0.89→0.92 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.73 / Num. unique all: 8139 / Χ2: 1.001 / % possible all: 75.6

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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 1Q0N

1q0n


Resolution: 0.89→23.202 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.06
Isotropic thermal model: Anisotropic for fully-occupied non-hydrogen atoms
Cross valid method: Throughout before the final 7 cycles of refinement
σ(F): 1.35 / Stereochemistry target values: ML
Details: The structure was refined for a total of 49 cycles, including 6 cycles with CNS, 20 cycles with SHELXL and 23 cycles with PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.128 100844 100 %Random
Rwork0.128 ---
obs0.128 100844 93.1 %-
all-100844 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.633 Å2 / ksol: 0.447 e/Å3
Displacement parametersBiso max: 91.76 Å2 / Biso mean: 12.849 Å2 / Biso min: 3.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.079 Å2-0 Å21.234 Å2
2--0.469 Å20 Å2
3----0.508 Å2
Refine analyzeLuzzati coordinate error obs: 0.006 Å
Refinement stepCycle: LAST / Resolution: 0.89→23.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 81 325 1673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093034
X-RAY DIFFRACTIONf_angle_d1.1535538
X-RAY DIFFRACTIONf_chiral_restr0.091229
X-RAY DIFFRACTIONf_plane_restr0.009480
X-RAY DIFFRACTIONf_dihedral_angle_d13.611811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
0.89-0.9220.25281200.252812016240812075
0.922-0.9590.18797240.187972419448972491
0.959-1.0020.15198920.151989219784989292
1.002-1.0550.1399970.13999719994999793
1.055-1.1210.123101190.12310119202381011994
1.121-1.2080.103103040.10310304206081030495
1.208-1.3290.104104200.10410420208401042096
1.329-1.5220.106105550.10610555211101055597
1.522-1.9170.116107300.11610730214601073099
1.917-23.210.126109830.12610983219661098399

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