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- PDB-2hsi: Crystal structure of putative peptidase M23 from pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 2hsi
TitleCrystal structure of putative peptidase M23 from pseudomonas aeruginosa, New York Structural Genomics Consortium
ComponentsPutative peptidase M23
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PEPTIDASE / PSI / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


septum digestion after cytokinesis / metalloendopeptidase activity / metal ion binding
Similarity search - Function
Peptidoglycan hydrolase domains / Peptidase family M23, N-terminal / Peptidase family M23 N-terminal domain / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Immunoglobulin-like ...Peptidoglycan hydrolase domains / Peptidase family M23, N-terminal / Peptidase family M23 N-terminal domain / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPatskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of M23 Peptidase from Pseudomonas Aeruginosa
Authors: Patskovsky, Y. / Ramagopal, U. / Almo, S.C.
History
DepositionJul 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_site
Item: _audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative peptidase M23
B: Putative peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7644
Polymers61,6332
Non-polymers1312
Water8,737485
1
A: Putative peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8822
Polymers30,8171
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8822
Polymers30,8171
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.313, 108.313, 83.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSERAA25 - 10425 - 104
21SERSERSERSERBB25 - 10425 - 104
12ASPASPGLNGLNAA126 - 281126 - 281
22ASPASPPHEPHEBB126 - 280126 - 280

NCS ensembles :
ID
1
2

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Components

#1: Protein Putative peptidase M23


Mass: 30816.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: PA3787 / Plasmid: TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXK8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.3 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 MM HEPES, 0.2 M AMMONIUM ACETATE, 25% PEG 3350, 10% GLYCEROL, PH 6.50, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 23, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 43712 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.065 / Rsym value: 0.048 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GU1

2gu1


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.523 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24522 1360 3.1 %RANDOM
Rwork0.20419 ---
obs0.20545 42302 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 2 485 3971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223580
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9754858
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1655461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59822.925147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60215573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1531528
X-RAY DIFFRACTIONr_chiral_restr0.1070.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022750
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1450.31752
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.52332
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.5659
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.356
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.548
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6872.52336
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.37533668
X-RAY DIFFRACTIONr_scbond_it5.5663.51385
X-RAY DIFFRACTIONr_scangle_it7.83951184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1624tight positional0.10.1
21067tight positional0.080.1
1624tight thermal0.41
21067tight thermal0.381
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 108 -
Rwork0.255 3061 -
obs--99.97 %

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