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- PDB-4zoq: Crystal Structure of a Lanthipeptide Protease -

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Basic information

Entry
Database: PDB / ID: 4zoq
TitleCrystal Structure of a Lanthipeptide Protease
Components(Intracellular serine protease) x 2
KeywordsHYDROLASE / serine protease / lanthipeptide
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
: / LicP N-terminal prodomain / Peptidase S8/S53 domain / : / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. ...: / LicP N-terminal prodomain / Peptidase S8/S53 domain / : / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Intracellular serine protease
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDong, S.H. / Nair, S.K.
CitationJournal: Chem Sci / Year: 2015
Title: Applications of the class II lanthipeptide protease LicP for sequence-specific, traceless peptide bond cleavage.
Authors: Tang, W. / Dong, S.H. / Repka, L.M. / He, C. / Nair, S.K. / van der Donk, W.A.
History
DepositionMay 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intracellular serine protease
I: Intracellular serine protease
B: Intracellular serine protease
J: Intracellular serine protease
C: Intracellular serine protease
K: Intracellular serine protease
D: Intracellular serine protease
L: Intracellular serine protease
E: Intracellular serine protease
M: Intracellular serine protease
F: Intracellular serine protease
N: Intracellular serine protease
G: Intracellular serine protease
O: Intracellular serine protease
H: Intracellular serine protease
P: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)388,73716
Polymers388,73716
Non-polymers00
Water19,8171100
1
A: Intracellular serine protease
I: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intracellular serine protease
J: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Intracellular serine protease
K: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Intracellular serine protease
L: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Intracellular serine protease
M: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Intracellular serine protease
N: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Intracellular serine protease
O: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Intracellular serine protease
P: Intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)48,5922
Polymers48,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.040, 112.780, 114.770
Angle α, β, γ (deg.)82.17, 89.68, 82.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Intracellular serine protease / LanP protein


Mass: 11094.953 Da / Num. of mol.: 8 / Fragment: UNP residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q65DC7
#2: Protein
Intracellular serine protease / LanP protein


Mass: 37497.156 Da / Num. of mol.: 8 / Fragment: UNP residues 101-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q65DC7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1100 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Precipitant of 20% PEG 3350, 2% tacsimate pH=7.0 and 4 mM HEPES pH=6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 143709 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 50.022 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.098 / Χ2: 0.977 / Net I/σ(I): 13.14 / Num. measured all: 568612
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.35-2.450.5940.8851.736711017229168431.02397.8
2.45-2.550.7110.6862.235654714494141870.79297.9
2.55-2.650.830.4873.114855212429121890.56298.1
2.65-2.750.890.3694.034191710736105240.42698
2.75-2.850.9230.2994.8736266926291090.34698.3
2.85-3.20.9740.1767.949392323960236120.20398.5
3.2-3.40.9890.10512.7237743964595150.12298.7
3.4-4.30.9970.05222.929506724327240960.06199.1
4.3-100.9990.03134.718486421934218010.03699.4
10-500.9990.02246.316623186918330.02698.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.1phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→38.031 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 7186 5 %
Rwork0.1995 --
obs0.202 143685 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→38.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24462 0 0 1100 25562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124941
X-RAY DIFFRACTIONf_angle_d1.54433746
X-RAY DIFFRACTIONf_dihedral_angle_d14.4359226
X-RAY DIFFRACTIONf_chiral_restr0.0663753
X-RAY DIFFRACTIONf_plane_restr0.0084365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37670.34362400.29214555X-RAY DIFFRACTION97
2.3767-2.40470.34012350.2774461X-RAY DIFFRACTION98
2.4047-2.4340.32152380.27754527X-RAY DIFFRACTION98
2.434-2.46480.32062380.26874525X-RAY DIFFRACTION98
2.4648-2.49720.32362390.2664527X-RAY DIFFRACTION98
2.4972-2.53140.29982380.2594533X-RAY DIFFRACTION98
2.5314-2.56760.3452370.26644506X-RAY DIFFRACTION98
2.5676-2.60590.3292390.25654537X-RAY DIFFRACTION98
2.6059-2.64660.3172370.24494506X-RAY DIFFRACTION98
2.6466-2.690.30892390.23994539X-RAY DIFFRACTION98
2.69-2.73630.28852410.24194576X-RAY DIFFRACTION98
2.7363-2.78610.32482340.23544452X-RAY DIFFRACTION98
2.7861-2.83970.31442420.24374585X-RAY DIFFRACTION98
2.8397-2.89760.30952370.2384515X-RAY DIFFRACTION98
2.8976-2.96060.27172420.22384593X-RAY DIFFRACTION99
2.9606-3.02940.29092370.22374508X-RAY DIFFRACTION98
3.0294-3.10520.2792420.22974588X-RAY DIFFRACTION99
3.1052-3.18910.27322400.22054563X-RAY DIFFRACTION99
3.1891-3.28290.25742390.21134544X-RAY DIFFRACTION99
3.2829-3.38880.25912420.21124604X-RAY DIFFRACTION99
3.3888-3.50980.28042390.20014524X-RAY DIFFRACTION99
3.5098-3.65020.24012400.18784563X-RAY DIFFRACTION99
3.6502-3.81620.24042400.17934569X-RAY DIFFRACTION99
3.8162-4.01720.21612420.17134584X-RAY DIFFRACTION99
4.0172-4.26860.21012400.16434569X-RAY DIFFRACTION99
4.2686-4.59760.18722410.15264579X-RAY DIFFRACTION99
4.5976-5.05930.2012430.15884612X-RAY DIFFRACTION99
5.0593-5.78920.22532410.17784577X-RAY DIFFRACTION99
5.7892-7.28540.21782420.18924596X-RAY DIFFRACTION100
7.2854-38.03610.20772420.17374582X-RAY DIFFRACTION99

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