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- PDB-7v9p: Crystal structure of the lanthipeptide zinc-metallopeptidase EryP... -

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Basic information

Entry
Database: PDB / ID: 7v9p
TitleCrystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in intermediate state
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: 1.8 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
B: Alanine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,6004
Polymers196,4692
Non-polymers1312
Water19,0601058
1
A: Alanine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3002
Polymers98,2341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alanine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3002
Polymers98,2341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.420, 66.630, 153.740
Angle α, β, γ (deg.)90.000, 93.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 98234.484 Da / Num. of mol.: 2
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.: 2 / 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.: 1058 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Sodium chloride, 0.1 M Tris ,pH 8.0, 20% 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: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→37.74 Å / Num. obs: 328585 / % possible obs: 98.9 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Num. unique obs: 11286 / CC1/2: 0.807 / Rpim(I) all: 0.308 / Rrim(I) all: 0.601 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V9N

7v9n


Resolution: 1.8→31.06 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2101 3911 1.19 %
Rwork0.19 324674 -
obs0.1903 328585 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.17 Å2 / Biso mean: 42.6222 Å2 / Biso min: 20.42 Å2
Refinement stepCycle: final / Resolution: 1.8→31.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13260 0 2 1058 14320
Biso mean--37.45 45.67 -
Num. residues----1695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.820.3791270.33419589971682
1.82-1.850.371540.3262102811043587
1.85-1.870.3748950.3039109761107192
1.87-1.890.33091610.2873115601172198
1.89-1.920.27661470.2707117441189199
1.92-1.950.31821370.2565118431198099
1.95-1.980.28291530.24541171611869100
1.98-2.010.26091360.2417117511188799
2.01-2.050.33121240.2333117651188999
2.05-2.090.20991520.2299117991195199
2.09-2.130.20971320.22971181911951100
2.13-2.170.21571380.2184117211185999
2.17-2.220.29761480.22171187812026100
2.22-2.270.23821580.21871172411882100
2.27-2.320.24711290.2231117161184599
2.32-2.390.24351380.21281189312031100
2.39-2.460.2511360.22131182711963100
2.46-2.540.23791550.21361171511870100
2.54-2.630.29691150.2117118311194699
2.63-2.730.24951440.2142117411188599
2.73-2.860.21461450.212117741191999
2.86-3.010.18691430.2065118121195599
3.01-3.20.20941350.2043117031183899
3.2-3.440.20571420.1795117221186499
3.44-3.790.18991440.1643117351187999
3.79-4.330.16931350.1432116851182099
4.33-5.460.15541460.1421117261187299
5.46-31.060.16791420.1595116281177098
Refinement TLS params.Method: refined / Origin x: 20.2313 Å / Origin y: -12.9454 Å / Origin z: 38.4521 Å
111213212223313233
T0.2361 Å20.0252 Å2-0.0095 Å2-0.2158 Å20.0011 Å2--0.2614 Å2
L0.2494 °20.0658 °2-0.0406 °2-0.4338 °2-0.0305 °2--0.8333 °2
S-0.0038 Å °0.0204 Å °-0.0377 Å °0.0028 Å °0.0251 Å °-0.0105 Å °0.0111 Å °-0.0308 Å °-0.0195 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 860
2X-RAY DIFFRACTION1allB3 - 860
3X-RAY DIFFRACTION1allS1 - 1189
4X-RAY DIFFRACTION1allC1 - 2

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