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- PDB-4mzd: High resolution crystal structure of the nisin leader peptidase N... -

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Basic information

Entry
Database: PDB / ID: 4mzd
TitleHigh resolution crystal structure of the nisin leader peptidase NisP from Lactococcus lactis
ComponentsNisin leader peptide-processing serine protease NisP
KeywordsHYDROLASE / alpha and beta proteins / subtilisin-like / serine protease
Function / homology
Function and homology information


cell wall / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / extracellular region
Similarity search - Function
Lantibiotic leader peptide-processing serine protease / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related ...Lantibiotic leader peptide-processing serine protease / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Leader peptide-processing serine protease / Nisin leader peptide-processing serine protease NisP
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsRao, Z.H. / Xu, Y.Y. / Li, X. / Yang, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the nisin leader peptidase NisP revealing a C-terminal autocleavage activity.
Authors: Xu, Y. / Li, X. / Li, R. / Li, S. / Ni, H. / Wang, H. / Xu, H. / Zhou, W. / Saris, P.E. / Yang, W. / Qiao, M. / Rao, Z.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Structure summary
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nisin leader peptide-processing serine protease NisP


Theoretical massNumber of molelcules
Total (without water)53,9501
Polymers53,9501
Non-polymers00
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.890, 44.973, 74.651
Angle α, β, γ (deg.)90.00, 106.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nisin leader peptide-processing serine protease NisP


Mass: 53949.652 Da / Num. of mol.: 1 / Fragment: UNP residues 196-682
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: nisP / Production host: Escherichia coli (E. coli)
References: UniProt: D9IXC0, UniProt: Q07596*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 1.49 Å3/Da / Density % sol: 17.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24-32% 1,4-dioxane, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2010
RadiationMonochromator: sagitally focused double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.1→71.459 Å / Num. obs: 128500 / % possible obs: 99.87 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 38.7
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.4 / % possible all: 95.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→26.947 Å / SU ML: 0.25 / σ(F): 1.89 / Phase error: 13.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1682 6301 5.03 %RANDOM
Rwork0.1517 ---
obs0.1525 128500 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.22 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1535 Å2-0 Å2-0.3095 Å2
2---0.8501 Å2-0 Å2
3---2.0036 Å2
Refinement stepCycle: LAST / Resolution: 1.1→26.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 0 454 3209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052910
X-RAY DIFFRACTIONf_angle_d1.0463963
X-RAY DIFFRACTIONf_dihedral_angle_d12.8761061
X-RAY DIFFRACTIONf_chiral_restr0.071425
X-RAY DIFFRACTIONf_plane_restr0.005529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11230.31143770.3126644X-RAY DIFFRACTION84
1.1123-1.12540.28963550.27357376X-RAY DIFFRACTION92
1.1254-1.13910.27424310.24477719X-RAY DIFFRACTION97
1.1391-1.15360.25623790.23257784X-RAY DIFFRACTION97
1.1536-1.16870.21844120.20657868X-RAY DIFFRACTION99
1.1687-1.18480.20593680.19227953X-RAY DIFFRACTION98
1.1848-1.20170.19454190.18137902X-RAY DIFFRACTION99
1.2017-1.21960.1964190.17147918X-RAY DIFFRACTION98
1.2196-1.23870.18363920.15717847X-RAY DIFFRACTION99
1.2387-1.2590.16194260.15087864X-RAY DIFFRACTION99
1.259-1.28070.16994100.14948012X-RAY DIFFRACTION99
1.2807-1.3040.15934320.14287856X-RAY DIFFRACTION99
1.304-1.32910.16114660.13337905X-RAY DIFFRACTION99
1.3291-1.35620.14064620.1277908X-RAY DIFFRACTION100
1.3562-1.38570.13454260.12137969X-RAY DIFFRACTION100
1.3857-1.41790.14883880.12457969X-RAY DIFFRACTION100
1.4179-1.45340.13854620.12587973X-RAY DIFFRACTION100
1.4534-1.49260.14144640.11747969X-RAY DIFFRACTION100
1.4926-1.53660.13784780.1147896X-RAY DIFFRACTION100
1.5366-1.58620.1474060.11857963X-RAY DIFFRACTION100
1.5862-1.64280.14173970.11678019X-RAY DIFFRACTION100
1.6428-1.70860.14674310.12668022X-RAY DIFFRACTION100
1.7086-1.78640.14344100.12677974X-RAY DIFFRACTION100
1.7864-1.88050.15124370.13517980X-RAY DIFFRACTION100
1.8805-1.99830.15473850.14127939X-RAY DIFFRACTION100
1.9983-2.15250.16663950.14818051X-RAY DIFFRACTION100
2.1525-2.3690.16564370.15397842X-RAY DIFFRACTION98
2.369-2.71160.16234210.15557974X-RAY DIFFRACTION100
2.7116-3.41520.16594080.15937883X-RAY DIFFRACTION99
3.4152-26.95510.20083050.16766254X-RAY DIFFRACTION78

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