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- PDB-8a28: Structure of the astacin zymogen of LAST-MAM from Limulus polyphemus -

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Basic information

Entry
Database: PDB / ID: 8a28
TitleStructure of the astacin zymogen of LAST-MAM from Limulus polyphemus
ComponentsMetalloendopeptidase
KeywordsHYDROLASE / metallopeptidase zymogen
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / zinc ion binding / membrane
Similarity search - Function
Astacin-like metallopeptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Metalloendopeptidase
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGuevara, T. / Rodriguez Banqueri, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Zymogenic latency in an ∼250-million-year-old astacin metallopeptidase.
Authors: Guevara, T. / Rodriguez-Banqueri, A. / Stocker, W. / Becker-Pauly, C. / Gomis-Ruth, F.X.
History
DepositionJun 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metalloendopeptidase
B: Metalloendopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6199
Polymers87,0242
Non-polymers5967
Water4,125229
1
A: Metalloendopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6944
Polymers43,5121
Non-polymers1823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metalloendopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9265
Polymers43,5121
Non-polymers4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.83, 47.57, 236.4
Angle α, β, γ (deg.)90, 102.91, 90
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metalloendopeptidase /


Mass: 43511.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab)
Gene: astl-mam / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: B4F320, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 6 types, 236 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Optimal crystals of protein at ~6.8 mg/mL in 50 mM HEPES pH 7.0 were obtained at 20 degrees with 0.1 M bicine pH 9.0, 10% polyethylene glycol (PEG) 40,000, 2% dioxane as the reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97244 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97244 Å / Relative weight: 1
ReflectionResolution: 2.4→76.8 Å / Num. obs: 49732 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.164 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.431 / Num. unique obs: 45644 / CC1/2: 0.594 / Rrim(I) all: 1.564 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.4→46.73 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.883 / SU R Cruickshank DPI: 0.251 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.221
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 741 -RANDOM
Rwork0.2534 ---
obs0.2538 49729 99.7 %-
Displacement parametersBiso mean: 77.61 Å2
Baniso -1Baniso -2Baniso -3
1-13.5518 Å20 Å2-3.5129 Å2
2--7.1832 Å20 Å2
3----20.735 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 32 229 5062
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0144963HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.266728HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2218SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes854HARMONIC5
X-RAY DIFFRACTIONt_it4963HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion597SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance10HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3497SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.94
X-RAY DIFFRACTIONt_other_torsion3.34
LS refinement shellResolution: 2.4→2.42 Å
RfactorNum. reflection% reflection
Rfree0.6035 30 -
Rwork0.4239 --
obs0.4278 1345 93.5 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.11860.3136-0.16758.06810.35650.05930.08440.0089-0.54230.0089-0.0919-0.393-0.5423-0.3930.0075-0.04780.21780.2061-0.33580.04830.00477.48621.7456.2774
24.0739-0.4017-0.6686.3343-0.17313.82310.123-0.9225-0.1034-0.9225-0.06180.0637-0.10340.0637-0.06120.04870.20790.1783-0.30050.1027-0.115417.542811.296347.539
33.9337-0.2619-0.20756.6947-1.42943.08060.1253-0.35920.1414-0.3592-0.0286-0.23150.1414-0.2315-0.0966-0.07870.19430.0656-0.30730.012-0.093814.5884-8.426555.8585
47.5587-8.84695.100233.2617-0.22821.941-0.12560.28610.17330.28610.53260.68030.17330.6803-0.40711.1147-0.25860.3966-0.17550.0694-0.319127.4084-5.727815.7837
53.9122-0.2932-3.48749.5836-2.804431.2145-0.34862.07891.51622.07890.6784-1.11351.5162-1.1135-0.32981.1537-0.08250.3164-0.12540.0196-0.360731.05022.2984-19.1635
69.417-2.969-1.533711.33870.45093.6210.5098-0.4162-0.3291-0.4162-0.2961-0.3873-0.3291-0.3873-0.2138-0.19930.19680.0902-0.25060.09580.119735.572535.287662.1002
76.3602-0.7457-1.54853.55930.4843.555-0.22660.76460.46180.76460.02980.24990.46180.24990.19690.11550.28430.1737-0.10140.18940.180635.801421.554670.918
88.1436-0.3943-1.10225.46881.52832.1525-0.02040.2884-0.19420.28840.1144-0.052-0.1942-0.052-0.094-0.15090.18750.0797-0.2036-0.03560.185848.094237.120362.8804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|22 - 56 }A22 - 56
2X-RAY DIFFRACTION2{A|57 - 149 }A57 - 149
3X-RAY DIFFRACTION2{A|57 - 149 }A501
4X-RAY DIFFRACTION3{A|150 - 244 }A150 - 244
5X-RAY DIFFRACTION4{A|245 - 256 }A245 - 256
6X-RAY DIFFRACTION5{A|257 - 403 }A257 - 403
7X-RAY DIFFRACTION6{B|22 - 56 }B22 - 56
8X-RAY DIFFRACTION7{B|57 - 149 }B57 - 149
9X-RAY DIFFRACTION7{B|57 - 149 }B501
10X-RAY DIFFRACTION8{B|150 - 246 }B150 - 246

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