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- PDB-5jip: Crystal structure of the Clostridium perfringens spore cortex lyt... -

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Basic information

Entry
Database: PDB / ID: 5jip
TitleCrystal structure of the Clostridium perfringens spore cortex lytic enzyme SleM
ComponentsCortical-lytic enzyme
KeywordsHYDROLASE / spore / cortex / peptidoglycan-lysin
Function / homology
Function and homology information


carbohydrate catabolic process / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cortical-lytic enzyme
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChirgadze, D.Y. / Christie, G. / Ustok, F.I. / Al-Riyami, B. / Stott, K.
CitationJournal: Proteins / Year: 2016
Title: The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germination.
Authors: Al-Riyami, B. / Ustok, F.I. / Stott, K. / Chirgadze, D.Y. / Christie, G.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cortical-lytic enzyme
B: Cortical-lytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9988
Polymers75,1692
Non-polymers8306
Water20,5191139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint1 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.599, 85.852, 87.205
Angle α, β, γ (deg.)90.00, 105.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cortical-lytic enzyme


Mass: 37584.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: sleM / Plasmid: pBADcLIC-SleM
Details (production host): arabinose inducible expression plasmid compatible with ligation independent cloning
Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: O06496
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1139 / 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: 2.44 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES buffer, pH 6.0, 0.25 M magnesium chloride, 16% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 5, 2014 / Details: HELIOS MX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→42.4 Å / Num. obs: 66317 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 24.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2313: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JFX

1jfx


Resolution: 1.8→42.397 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.01
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 3364 5.08 %Random
Rwork0.151 ---
obs0.1526 66248 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 50 1140 6242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015235
X-RAY DIFFRACTIONf_angle_d1.0657100
X-RAY DIFFRACTIONf_dihedral_angle_d13.7043107
X-RAY DIFFRACTIONf_chiral_restr0.058742
X-RAY DIFFRACTIONf_plane_restr0.007920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82570.30171270.27472532X-RAY DIFFRACTION98
1.8257-1.8530.31591200.24862606X-RAY DIFFRACTION98
1.853-1.88190.28841460.22962579X-RAY DIFFRACTION98
1.8819-1.91280.26141280.20162571X-RAY DIFFRACTION99
1.9128-1.94580.21051390.1822631X-RAY DIFFRACTION99
1.9458-1.98120.23421500.1842566X-RAY DIFFRACTION99
1.9812-2.01930.21961600.17152602X-RAY DIFFRACTION100
2.0193-2.06050.23711340.16912569X-RAY DIFFRACTION100
2.0605-2.10530.20571680.16492655X-RAY DIFFRACTION100
2.1053-2.15420.19241260.1522603X-RAY DIFFRACTION100
2.1542-2.20810.18621330.14782658X-RAY DIFFRACTION100
2.2081-2.26780.18071390.15122587X-RAY DIFFRACTION100
2.2678-2.33450.17781390.14352633X-RAY DIFFRACTION100
2.3345-2.40990.17261680.14092632X-RAY DIFFRACTION100
2.4099-2.4960.17051450.14262621X-RAY DIFFRACTION100
2.496-2.59590.17451380.13272611X-RAY DIFFRACTION100
2.5959-2.71410.1631570.13312621X-RAY DIFFRACTION100
2.7141-2.85710.18491190.13612659X-RAY DIFFRACTION100
2.8571-3.03610.13731370.13272643X-RAY DIFFRACTION100
3.0361-3.27040.16831530.13692613X-RAY DIFFRACTION100
3.2704-3.59940.16891370.12942667X-RAY DIFFRACTION100
3.5994-4.11980.12641320.12452635X-RAY DIFFRACTION100
4.1198-5.18910.14251340.11992667X-RAY DIFFRACTION100
5.1891-42.3970.17141350.17292723X-RAY DIFFRACTION100

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