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- PDB-3ki9: Crystal structure of Staphylococcus aureus metallopeptidase (Sape... -

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Basic information

Entry
Database: PDB / ID: 3ki9
TitleCrystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the Mn2+ bound form
ComponentsPutative dipeptidase SACOL1801
KeywordsHYDROLASE / Mn+2 bound form-Dipeptidase (DapE) / Metallopeptidase / Sapep / M20 peptidase / Dipeptidase / Metal-binding / Metalloprotease / Protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / dipeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Peptidase M20A, peptidase V-related / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Putative dipeptidase SACOL1801
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGirish, T.S. / Gopal, B.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states
Authors: Girish, T.S. / Gopal, B.
History
DepositionNov 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative dipeptidase SACOL1801
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5454
Polymers55,3401
Non-polymers2053
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.150, 158.150, 158.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Putative dipeptidase SACOL1801 / Metallopeptidase / DapE


Mass: 55339.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: dipeptidase PepV(SACOL1801) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5HF23, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: microbatch method under oil / pH: 6.8
Details: 0.2M Megnesium Acetate tetrahydrate, 0.1M Sodium Cacodylate pH 6.8, 22.0% Polyethylene glycol 8000, Microbatch method under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 14758 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Biso Wilson estimate: 69.9 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.115 / Net I/σ(I): 14.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2141 / Rsym value: 0.604 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KHX, independent domains

3khx


Resolution: 2.9→28.88 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.877 / SU B: 29.04 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 745 5.1 %RANDOM
Rwork0.20212 ---
obs0.20492 13998 99.99 %-
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: 42.555 Å2
Refine analyzeLuzzati coordinate error free: 0.398 Å
Refinement stepCycle: LAST / Resolution: 2.9→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 7 26 3695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223735
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.9465064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8455464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88825.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34515603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.691514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212902
X-RAY DIFFRACTIONr_mcbond_it0.3041.52311
X-RAY DIFFRACTIONr_mcangle_it0.57723707
X-RAY DIFFRACTIONr_scbond_it0.69531424
X-RAY DIFFRACTIONr_scangle_it1.2324.51357
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 45 -
Rwork0.327 1024 -
obs-1024 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.970.001-0.20671.1052-0.11970.66260.08720.0660.08350.0618-0.08370.0483-0.0637-0.021-0.00350.0527-0.00880.02660.0144-0.00350.017951.9904-29.55875.0527
20.813-0.3473-0.12681.77220.22761.06270.0334-0.1002-0.08340.0864-0.0556-0.12330.0040.07940.02220.0187-0.0199-0.00960.0320.01870.025957.6076-61.021218.0286
30.8729-0.8301-0.30761.3261-0.27481.32010.0276-0.0565-0.00970.05440.05490.1598-0.0504-0.1069-0.08240.0252-0.01370.03320.029-0.01490.054138.9555-33.004812.7438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 182
2X-RAY DIFFRACTION2A184 - 383
3X-RAY DIFFRACTION3A385 - 464

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