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- PDB-7v9o: Crystal structure of the lanthipeptide zinc-metallopeptidase EryP... -

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Basic information

Entry
Database: PDB / ID: 7v9o
TitleCrystal structure of the lanthipeptide zinc-metallopeptidase EryP mutant E802R from saccharopolyspora erythraea
ComponentsAlanine aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / Alanine aminopeptidase / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / proteolysis / extracellular space / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Peptidase M1, aminopeptidase / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / 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
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)98,5233
Polymers98,2631
Non-polymers2612
Water22,5551252
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area30650 Å2
Unit cell
Length a, b, c (Å)58.909, 143.583, 60.580
Angle α, β, γ (deg.)90.000, 114.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 98262.562 Da / Num. of mol.: 1 / Mutation: E802R
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
#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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1252 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v), PEG 6000, MES 6.0, 200mM Ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.77→19.86 Å / Num. obs: 88457 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.032 / Rrim(I) all: 0.085 / Net I/σ(I): 16.1 / Num. measured all: 597759
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.77-1.86.30.3222812144990.9490.1380.351599.8
9.53-19.867.20.0438265290.9990.0160.04335.689.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V9N

7v9n


Resolution: 1.77→19.57 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1706 2003 2.27 %RANDOM
Rwork0.139 86411 --
obs0.1397 88414 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 16.633 Å2 / Biso min: 8.69 Å2
Refinement stepCycle: final / Resolution: 1.77→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 13 1252 8006
Biso mean--23.05 25.96 -
Num. residues----860
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.810.26151340.170361306264100
1.81-1.860.19681530.15461516304100
1.86-1.920.18321380.145461836321100
1.92-1.980.18891420.145561456287100
1.98-2.050.19331480.141461896337100
2.05-2.130.17561360.137761656301100
2.13-2.230.15961450.135561586303100
2.23-2.350.16031410.142362006341100
2.35-2.490.17491460.14461486294100
2.49-2.690.17381390.141862106349100
2.69-2.960.18441480.141561426290100
2.96-3.380.16121410.136862026343100
3.38-4.250.14361480.1246147629599
4.25-19.570.16451440.13762416385100
Refinement TLS params.Method: refined / Origin x: -25.558 Å / Origin y: -23.8583 Å / Origin z: 76.3137 Å
111213212223313233
T0.0978 Å20.0002 Å2-0.0069 Å2-0.1034 Å2-0.002 Å2--0.0931 Å2
L0.1944 °20.0231 °2-0.0674 °2-0.1792 °2-0.0254 °2--0.1576 °2
S-0.0071 Å °-0.0014 Å °-0.0243 Å °-0.0156 Å °-0.002 Å °0.0027 Å °0.0171 Å °0.0006 Å °0.0089 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1
2X-RAY DIFFRACTION1allS1 - 1371
3X-RAY DIFFRACTION1allA1 - 860
4X-RAY DIFFRACTION1allC901

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