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- PDB-1ad1: DIHYDROPTEROATE SYNTHETASE (APO FORM) FROM STAPHYLOCOCCUS AUREUS -

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Basic information

Entry
Database: PDB / ID: 1ad1
TitleDIHYDROPTEROATE SYNTHETASE (APO FORM) FROM STAPHYLOCOCCUS AUREUS
ComponentsDIHYDROPTEROATE SYNTHETASE
KeywordsTRANSFERASE / SYNTHETASE / DIHYDROPTEROATE SYNTHETASE / DHPS / APO FORM / COMPLEX WITH OH-CH2-PTERIN-PYROPHOSPHATE
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / response to antibiotic / metal ion binding
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
: / Dihydropteroate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsKostrewa, D. / Oefner, C. / D'Arcy, A.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Structure and function of the dihydropteroate synthase from Staphylococcus aureus.
Authors: Hampele, I.C. / D'Arcy, A. / Dale, G.E. / Kostrewa, D. / Nielsen, J. / Oefner, C. / Page, M.G. / Schonfeld, H.J. / Stuber, D. / Then, R.L.
History
DepositionFeb 19, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPTEROATE SYNTHETASE
B: DIHYDROPTEROATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0055
Polymers58,8052
Non-polymers2003
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-14 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.470, 42.190, 101.320
Angle α, β, γ (deg.)90.00, 106.33, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE DIMER.

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Components

#1: Protein DIHYDROPTEROATE SYNTHETASE / DHPS


Mass: 29402.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: APO FORM / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: O05701, dihydropteroate synthase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-16 %(v/w)PEG40001reservoir
2200 mMsodium potassium tartrate1reservoir
3100 mMbis-tris1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A
DetectorDate: Aug 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 13.5 Å / Num. obs: 23614 / % possible obs: 88 % / Num. measured all: 74289 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 69 %

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.2→13.5 Å / σ(F): 0
Details: CONVENTIONAL RESTRAINED POSITIONAL AND TEMPERATURE FACTOR REFINEMENT WITH STEREOCHEMICAL PARAMETERS FROM ENGH & HUBER. THE ELECTRON DENSITY OF THE TRIS MOLECULE IS ONLY POORLY DEFINED.
RfactorNum. reflection
Rfree0.218 -
Rwork0.159 -
obs0.159 23608
Refinement stepCycle: LAST / Resolution: 2.2→13.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3984 0 10 401 4395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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