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- PDB-7v9q: Crystal structure of the lanthipeptide zinc-metallopeptidase EryP... -

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Basic information

Entry
Database: PDB / ID: 7v9q
TitleCrystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in open state
ComponentsAlanine aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / Alanine aminopeptidase / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding
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: 2.67 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

Downloads & links

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Assembly

Deposited unit
A: Alanine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3002
Polymers98,2341
Non-polymers651
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area33760 Å2
Unit cell
Length a, b, c (Å)58.818, 111.577, 156.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Citric acid , pH 3.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 30085 / % possible obs: 99.7 % / Redundancy: 10 % / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.063 / Rrim(I) all: 0.205 / Χ2: 0.722 / Net I/σ(I): 2.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.67-2.729.20.73214670.6580.2480.7750.33698.9
2.72-2.779.20.71214420.6360.240.7530.33999.2
2.77-2.829.30.67314960.6960.2270.7110.34199.3
2.82-2.889.30.62914650.7370.2140.6650.35599.8
2.88-2.949.30.56915080.8010.1920.6010.37399.8
2.94-3.019.40.53514740.8350.1810.5650.38499.5
3.01-3.089.40.47114760.8770.1590.4980.39599.7
3.08-3.179.10.42814690.8890.1470.4530.43199.5
3.17-3.269.30.35414980.9330.120.3750.45499.3
3.26-3.369.60.31614670.9540.1050.3340.599.7
3.36-3.4810.60.29615140.9640.0930.3110.56699.7
3.48-3.6210.90.23615000.9780.0730.2480.576100
3.62-3.79110.19714870.9860.0610.2060.60399.9
3.79-3.99110.20415050.9890.0630.2140.63999.9
3.99-4.24110.12815080.9930.0390.1340.679100
4.24-4.5610.40.10715290.9960.0340.1130.59599.9
4.56-5.0210.10.09615240.9940.0310.1010.69499.9
5.02-5.7511.30.10415360.9940.0320.1090.698100
5.75-7.24110.10415680.9930.0320.1090.881100
7.24-50100.11116520.9610.0370.1173.99499.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V9N

7v9n


Resolution: 2.67→36.18 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 1995 6.65 %
Rwork0.2017 27996 -
obs0.2026 29991 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.4 Å2 / Biso mean: 52.6688 Å2 / Biso min: 14.94 Å2
Refinement stepCycle: final / Resolution: 2.67→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 1 131 6852
Biso mean--32.11 45.08 -
Num. residues----859
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 (%)
2.66-2.730.28981340.26651879201397
2.73-2.80.29691430.27462007215099
2.8-2.890.29981380.267319412079100
2.89-2.980.28581410.254819692110100
2.98-3.090.29131440.242220092153100
3.09-3.210.26061390.23741955209499
3.21-3.360.22591410.214919822123100
3.36-3.530.24861430.212519982141100
3.53-3.750.2161420.194220002142100
3.75-4.040.18211440.170919992143100
4.04-4.450.16521450.162320442189100
4.45-5.090.18041440.160920222166100
5.09-6.410.16831480.194320592207100
6.41-36.180.19891490.19122132228198
Refinement TLS params.Method: refined / Origin x: 18.6897 Å / Origin y: -0.6455 Å / Origin z: -14.2187 Å
111213212223313233
T0.1441 Å2-0.0209 Å20.013 Å2-0.1809 Å20.0008 Å2--0.17 Å2
L0.3238 °2-0.2108 °2-0.3484 °2-0.8001 °20.2612 °2--0.5899 °2
S-0.0669 Å °-0.0255 Å °-0.0576 Å °-0.0661 Å °0.0224 Å °0.0189 Å °0.1578 Å °-0.0347 Å °-0.0124 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 860
2X-RAY DIFFRACTION1allB1 - 277
3X-RAY DIFFRACTION1allC1

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