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- PDB-7v9n: Crystal structure of the lanthipeptide zinc-metallopeptidase EryP... -

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Basic information

Entry
Database: PDB / ID: 7v9n
TitleCrystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in closed state
ComponentsAlanine aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / Alanine aminopeptidase / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / proteolysis / zinc ion binding / cytoplasm
Similarity search - Function
Peptidase M1, aminopeptidase / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily
Similarity search - Domain/homology
ACETATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhao, C. / Zhao, N.L. / Bao, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Conformational remodeling enhances activity of lanthipeptide zinc-metallopeptidases.
Authors: Zhao, C. / Sheng, W. / Wang, Y. / Zheng, J. / Xie, X. / Liang, Y. / Wei, W. / Bao, R. / Wang, H.
History
DepositionAug 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6757
Polymers98,2341
Non-polymers4416
Water14,340796
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.577, 153.577, 98.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1289-

HOH

21A-1483-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alanine aminopeptidase / Aminopeptidase N / Lysyl aminopeptidase


Mass: 98234.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338) (bacteria)
Strain: ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338
Gene: SACE_1339, A8924_1736 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4F9D7, membrane alanyl aminopeptidase

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Non-polymers , 5 types, 802 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M calcium acetate, 0.1 M sodium acetate, pH 4.5, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→39.09 Å / Num. obs: 92705 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.025 / Rrim(I) all: 0.128 / Net I/σ(I): 25.2
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.758 / Num. unique obs: 4506 / CC1/2: 0.982 / Rpim(I) all: 0.149 / Rrim(I) all: 0.772 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.08 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 2000 2.16 %RANDOM
Rwork0.1538 90587 --
obs0.1544 92587 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.31 Å2 / Biso mean: 28.26 Å2 / Biso min: 11.83 Å2
Refinement stepCycle: final / Resolution: 1.9→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6732 0 24 796 7552
Biso mean--36.69 36.7 -
Num. residues----859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.950.21951400.199763566496
1.95-20.21361410.176264056546
2-2.060.19551410.169963746515
2.06-2.130.20351420.159664026544
2.13-2.20.19571410.161364116552
2.2-2.290.20151420.156164486590
2.29-2.390.23031420.154564006542
2.39-2.520.20041420.156764266568
2.52-2.680.2291410.157964416582
2.68-2.880.17431440.155464726616
2.88-3.170.1951430.158664956638
3.17-3.630.16861440.153665266670
3.63-4.580.14811460.130466016747
4.58-32.080.1561510.155368306981
Refinement TLS params.Method: refined / Origin x: -8.4004 Å / Origin y: -41.4405 Å / Origin z: 18.2759 Å
111213212223313233
T0.1117 Å20.0112 Å2-0.0173 Å2-0.1275 Å2-0.0098 Å2--0.1061 Å2
L0.3807 °20.1914 °20.1584 °2-0.2166 °20.1259 °2--0.1481 °2
S-0.0128 Å °-0.0236 Å °0.0514 Å °-0.005 Å °-0.0222 Å °0.0277 Å °0 Å °-0.0211 Å °-0.0921 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 860
2X-RAY DIFFRACTION1allB4
3X-RAY DIFFRACTION1allC3
4X-RAY DIFFRACTION1allE1 - 3
5X-RAY DIFFRACTION1allF1
6X-RAY DIFFRACTION1allS1 - 874

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