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- PDB-1g4c: CRYSTAL STRUCTURE OF A COMPLEX OF HPPK(R92A) FROM E.COLI WITH MG2... -

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Basic information

Entry
Database: PDB / ID: 1g4c
TitleCRYSTAL STRUCTURE OF A COMPLEX OF HPPK(R92A) FROM E.COLI WITH MG2+ AT 1.65 ANGSTROM RESOLUTION
Components6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
KeywordsTRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / PTERIN / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN / ANTIMICROBIAL AGENT / DRUG DESIGN
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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-dihydropterin Pyrophosphokinase: Crystallographic Studies
Authors: BLASZCZYK, J. / Li, Y. / SHI, G. / YAN, H. / JI, X.
#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.
#2: 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
DepositionOct 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
B: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9408
Polymers35,7612
Non-polymers1796
Water7,638424
1
A: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9764
Polymers17,8801
Non-polymers953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9644
Polymers17,8801
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.351, 47.210, 71.306
Angle α, β, γ (deg.)90.00, 105.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE / 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE / HPPK


Mass: 17880.418 Da / Num. of mol.: 2 / Mutation: R92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET17B / Production host: Escherichia coli (E. coli)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 33.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG4000, MAGNESIUM CHLORIDE, TRIS-HCL, ACETATE, GLYCEROL, pH 8.40, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal grow
*PLUS
Temperature: 18-20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
330 %(w/v)PEG40001reservoir
4200 mMsodium acetate1reservoir
550 mM1reservoirMgCl2
6100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.009
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2000 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 32443 / Num. obs: 32443 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.73 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.9123
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.431 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2 / Num. unique all: 3203 / % possible all: 98
Reflection
*PLUS
Num. measured all: 88579
Reflection shell
*PLUS
% possible obs: 98 % / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1HKA

1hka


Resolution: 1.65→30 Å / Num. parameters: 10355 / Num. restraintsaints: 10586 / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
Details: LEAST-SQUARES REFINEMENT USING THE KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1659 5.3953 %RANDOM
Rwork0.172 ---
all0.2048 30749 --
obs0.1957 22944 93.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1975) 201-228
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 2476 / Occupancy sum non hydrogen: 2947
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 6 425 2963
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.051
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.069
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.236 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.025
X-RAY DIFFRACTIONs_chiral_restr0.065

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