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- PDB-1qxw: Crystal structure of Staphyloccocus aureus in complex with an ami... -

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Basic information

Entry
Database: PDB / ID: 1qxw
TitleCrystal structure of Staphyloccocus aureus in complex with an aminoketone inhibitor 54135.
Componentsmethionyl aminopeptidase
KeywordsHYDROLASE / pita bread fold
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / (3S)-3-AMINO-1-(CYCLOPROPYLAMINO)HEPTANE-2,2-DIOL / Methionine aminopeptidase / Methionine aminopeptidase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsDouangamath, A. / Dale, G.E. / D'Arcy, A. / Oefner, C.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Crystal structures of staphylococcusaureus methionine aminopeptidase complexed with keto heterocycle and aminoketone inhibitors reveal the formation of a tetrahedral intermediate.
Authors: Douangamath, A. / Dale, G.E. / D'Arcy, A. / Almstetter, M. / Eckl, R. / Frutos-Hoener, A. / Henkel, B. / Illgen, K. / Nerdinger, S. / Schulz, H. / MacSweeney, A. / Thormann, M. / Treml, A. / ...Authors: Douangamath, A. / Dale, G.E. / D'Arcy, A. / Almstetter, M. / Eckl, R. / Frutos-Hoener, A. / Henkel, B. / Illgen, K. / Nerdinger, S. / Schulz, H. / MacSweeney, A. / Thormann, M. / Treml, A. / Pierau, S. / Wadman, S. / Oefner, C.
History
DepositionSep 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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
Remark 600heterogen The original inhibitor used in the crystal was 3-Amino-1-cyclopropylamino-heptan-2-one. ...heterogen The original inhibitor used in the crystal was 3-Amino-1-cyclopropylamino-heptan-2-one. The M1C coordinates in this structure are those of a transition state complex of the inhibitor.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: methionyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9746
Polymers27,5351
Non-polymers4385
Water7,044391
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.993, 76.843, 41.935
Angle α, β, γ (deg.)90.00, 104.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein methionyl aminopeptidase


Mass: 27535.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: aureus Mu50 / Plasmid: PDS56-RBSII / Production host: Escherichia coli (E. coli)
References: UniProt: P0A080, UniProt: P0A078*PLUS, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-M1C / (3S)-3-AMINO-1-(CYCLOPROPYLAMINO)HEPTANE-2,2-DIOL


Mass: 202.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5
Details: PEG 3350, Bis-tris, ammonium acetate, pH 5.5, microbatch, temperature 294K
Crystal grow
*PLUS
pH: 7.5 / Method: batch method / Details: Oefner, C., (2003) J. Mol. Biol., 332, 13.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein11
250 mMHEPES11pH7.5
3150 mM11NaCl
45 %glycerol11
51 mMTCEP11

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.57 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 2002
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.57 Å / Relative weight: 1
ReflectionResolution: 1.67→20 Å / Num. all: 29574 / Num. obs: 29278 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 14 Å2 / Net I/σ(I): 28
Reflection shellResolution: 1.67→1.77 Å / Mean I/σ(I) obs: 8.6 / % possible all: 96.7
Reflection
*PLUS
Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.117

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.315 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18525 1469 5.1 %RANDOM
Rwork0.15808 ---
all0.1594 29278 --
obs0.15945 27514 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.793 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.46 Å2
2---0.17 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.67→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 24 391 2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221955
X-RAY DIFFRACTIONr_bond_other_d0.0010.021781
X-RAY DIFFRACTIONr_angle_refined_deg2.0831.9652644
X-RAY DIFFRACTIONr_angle_other_deg0.64134180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9083247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.0415366
X-RAY DIFFRACTIONr_chiral_restr0.0670.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022138
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02337
X-RAY DIFFRACTIONr_nbd_refined0.2420.3410
X-RAY DIFFRACTIONr_nbd_other0.1890.31771
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.5324
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1550.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.530
X-RAY DIFFRACTIONr_mcbond_it0.5021.51242
X-RAY DIFFRACTIONr_mcangle_it0.93722008
X-RAY DIFFRACTIONr_scbond_it1.6273713
X-RAY DIFFRACTIONr_scangle_it2.7774.5633
LS refinement shellResolution: 1.67→1.76 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.242 216
Rwork0.214 3897
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.185 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.082

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