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- PDB-1eye: 1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-... -

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Basic information

Entry
Database: PDB / ID: 1eye
Title1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTEROATE SYNTHASE (DHPS) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 6-HYDROXYMETHYLPTERIN MONOPHOSPHATE
ComponentsDIHYDROPTEROATE SYNTHASE I
KeywordsTRANSFERASE / alpha-beta barrel
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PTERIN-6-YL-METHYL-MONOPHOSPHATE / Dihydropteroate synthase / Dihydropteroate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBaca, A.M. / Sirawaraporn, R. / Turley, S. / Sirawaraporn, W. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of Mycobacterium tuberculosis 7,8-dihydropteroate synthase in complex with pterin monophosphate: new insight into the enzymatic mechanism and sulfa-drug action.
Authors: Baca, A.M. / Sirawaraporn, R. / Turley, S. / Sirawaraporn, W. / Hol, W.G.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPTEROATE SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1703
Polymers28,8731
Non-polymers2972
Water4,396244
1
A: DIHYDROPTEROATE SYNTHASE I
hetero molecules

A: DIHYDROPTEROATE SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3416
Polymers57,7462
Non-polymers5954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4280 Å2
ΔGint-53 kcal/mol
Surface area20350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.900, 62.900, 121.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein DIHYDROPTEROATE SYNTHASE I / DHPS 1


Mass: 28872.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Plasmid: PKOS007-90 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A578, UniProt: P9WND1*PLUS, dihydropteroate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Details: PtP was synthesized from 6-hydroxymethyl pterin and pyrophosphoric acid as described by Shiota et al., 1964
#3: Chemical ChemComp-PMM / PTERIN-6-YL-METHYL-MONOPHOSPHATE


Mass: 273.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N5O5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 4000, Sodium Acetate, Ammonium Acetate, para-aminosalicylic acid, 6-hydroxymethl pterin monophosphate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate1reservoir
2200 mMammonium acetate1reservoir
330 %(w/v)PEG40001reservoir
43 mMPtP1reservoir
53 mMpABA1reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→26.5 Å / Num. all: 136341 / Num. obs: 25211 / % possible obs: 80.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 20.649 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 32.411
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.177 / Num. unique all: 2137 / % possible all: 69.9
Reflection
*PLUS
Num. measured all: 136341
Reflection shell
*PLUS
% possible obs: 69.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNTrefinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT default
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1236 -RANDOM
Rwork0.185 ---
all0.185 25211 --
obs0.185 25211 80.5 %-
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 19 244 2110
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.6
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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