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- PDB-4i35: The crystal structure of serralysin -

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Basic information

Entry
Database: PDB / ID: 4i35
TitleThe crystal structure of serralysin
ComponentsSerralysin
KeywordsHYDROLASE / Amino Acid Sequence / Binding Sites / Calcium / Metalloendopeptidases / Protein Structure / 1. zincin like 2. Single-stranded right-handed beta-helix / metal ion binding / extracellular
Function / homology
Function and homology information


serralysin / symbiont-mediated killing of host cell / extracellular matrix / metalloendopeptidase activity / toxin activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat ...Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HEXANE / N-OCTANE / Serralysin
Similarity search - Component
Biological speciesserratia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsZou, M. / Ran, T. / Xu, D. / Wang, W.
CitationJournal: To be Published
Title: The crystal structure of serralysin
Authors: Wang, W. / Xu, D. / Zou, M. / Ran, T.
History
DepositionNov 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_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: Serralysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,50418
Polymers50,2971
Non-polymers1,20717
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.357, 105.075, 151.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serralysin /


Mass: 50297.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) serratia (bacteria) / Strain: FS14 / References: UniProt: P23694*PLUS

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Non-polymers , 6 types, 593 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6.3
Details: 30% peg8000, 0.1M ammonium sulfate, 0.1M citrate, pH 6.3, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9799 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.501→37.779 Å / Num. all: 108563 / Num. obs: 108473 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.501→37.779 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 15.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.165 5415 4.99 %Random
Rwork0.1483 ---
obs0.1491 108473 99.76 %-
all-108563 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→37.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 66 576 4203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193782
X-RAY DIFFRACTIONf_angle_d1.2025198
X-RAY DIFFRACTIONf_dihedral_angle_d13.6521288
X-RAY DIFFRACTIONf_chiral_restr0.076526
X-RAY DIFFRACTIONf_plane_restr0.006680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.501-1.51810.22071630.1929334798
1.5181-1.53590.1831960.17683367100
1.5359-1.55460.1912070.17363376100
1.5546-1.57430.18311750.16573427100
1.5743-1.5950.1981770.1693361100
1.595-1.61690.17761910.16223412100
1.6169-1.640.21291910.15843389100
1.64-1.66450.181680.1563398100
1.6645-1.69050.17891550.14853474100
1.6905-1.71820.16071690.14713385100
1.7182-1.74780.15011520.14233438100
1.7478-1.77960.15741980.14663370100
1.7796-1.81380.17391860.14543386100
1.8138-1.85090.17381660.1473457100
1.8509-1.89110.17441790.14463393100
1.8911-1.93510.17511800.14823444100
1.9351-1.98350.16441830.14523405100
1.9835-2.03710.16281670.14213439100
2.0371-2.0970.15772000.14633411100
2.097-2.16470.14291700.14213423100
2.1647-2.24210.17351770.13963468100
2.2421-2.33180.16251810.14323438100
2.3318-2.43790.19711750.14333438100
2.4379-2.56650.15311790.14593459100
2.5665-2.72720.17121950.14743440100
2.7272-2.93770.13981610.15313529100
2.9377-3.23320.17262030.15763490100
3.2332-3.70070.15311810.14593497100
3.7007-4.66110.13612010.13093547100
4.6611-37.79050.18571890.1592365098

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