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- PDB-3hd1: Crystal structure of E. coli HPPK(N10A) in complex with MgAMPCPP -

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Basic information

Entry
Database: PDB / ID: 3hd1
TitleCrystal structure of E. coli HPPK(N10A) in complex with MgAMPCPP
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 / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 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: J.Biol.Chem. / Year: 2001
Title: Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR.
Authors: Xiao, B. / Shi, G. / Gao, J. / Blaszczyk, J. / Liu, Q. / Ji, X. / Yan, H.
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 / 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: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5726
Polymers17,9241
Non-polymers6485
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.830, 53.020, 36.600
Angle α, β, γ (deg.)90.00, 102.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-245-

HOH

21A-460-

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: 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

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Non-polymers , 5 types, 292 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.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
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: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 1999 / Details: mirrors
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. all: 36325 / Num. obs: 36325 / % possible obs: 99.1 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.48 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.099 / Χ2: 0.935 / Net I/σ(I): 11.361
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.51 / Num. unique all: 3548 / Χ2: 0.734 / % possible all: 97.6

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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 1EQM

1eqm


Resolution: 1.3→21.289 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.827 / SU ML: 0.2
Isotropic thermal model: Anisotropic for atoms whose OCC=1.0
Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
Details: The structure was refined for a total of 42 cycles, including 6 cycles with CNS, 29 cycles with SHELX, and 7 cycles with PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.22 999 2.75 %Random
Rwork0.167 ---
obs0.168 36305 98.93 %-
all-36305 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.112 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso max: 59.93 Å2 / Biso mean: 20.429 Å2 / Biso min: 1.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.374 Å20 Å2-2.635 Å2
2--1.536 Å20 Å2
3----3.106 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.3→21.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 38 287 1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041476
X-RAY DIFFRACTIONf_angle_d0.9292040
X-RAY DIFFRACTIONf_chiral_restr0.062220
X-RAY DIFFRACTIONf_plane_restr0.004273
X-RAY DIFFRACTIONf_dihedral_angle_d15.988583
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 (%)
1.3-1.3680.31400.26549395079507997
1.368-1.4540.2541410.21949805121512198
1.454-1.5660.2491420.1850075149514999
1.566-1.7240.2181420.16150435185518599
1.724-1.9730.2341440.144508052245224100
1.973-2.4860.1991440.142510152455245100
2.486-21.2920.2011460.15751565302530299

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