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- PDB-6ghx: Alzheimer's Amyloid-Beta Peptide Fragment 31-35 in Complex with C... -

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Basic information

Entry
Database: PDB / ID: 6ghx
TitleAlzheimer's Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd-substituted Thermolysin
ComponentsThermolysin
KeywordsHYDROLASE / peptidase / protein-peptide complex
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / ISOLEUCINE / Thermolysin
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.156 Å
AuthorsLeite, J.P. / Gales, L.
Funding support Portugal, 1items
OrganizationGrant numberCountry
SFRH/BD/129921/2017 Portugal
CitationJournal: FEBS Lett. / Year: 2019
Title: Alzheimer's A beta1-40peptide degradation by thermolysin: evidence of inhibition by a C-terminal A beta product.
Authors: Leite, J.P. / Gales, L.
History
DepositionMay 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9749
Polymers34,3601
Non-polymers6138
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-58 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.060, 93.060, 130.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-738-

HOH

21A-779-

HOH

31A-829-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thermolysin / Neutral protease


Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P43133, thermolysin

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Non-polymers , 5 types, 375 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.73 % / Mosaicity: 0.06 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 6
Details: 50 mM MES: 45% DMSO: 0.7-0.9 M NaCl: 0-0.4 M CdCl2: reservoir solution containing 30-40% ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2018
Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 1.16→46.53 Å / Num. obs: 114872 / % possible obs: 100 % / Redundancy: 17.3 % / Biso Wilson estimate: 17.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.017 / Rrim(I) all: 0.074 / Net I/σ(I): 17.2 / Num. measured all: 1989653 / Scaling rejects: 2
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
1.16-1.216.42.785182165111050.4650.7032.8740.8100
4.49-46.5317.90.0424037722620.9980.010.04364.299.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1kei

1kei


Resolution: 1.156→46.53 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 5744 4.99 %
Rwork0.2016 109329 -
obs0.2025 115073 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.87 Å2 / Biso mean: 23.7965 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 1.156→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 25 367 2840
Biso mean--26.97 36.96 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052541
X-RAY DIFFRACTIONf_angle_d0.8243469
X-RAY DIFFRACTIONf_chiral_restr0.081373
X-RAY DIFFRACTIONf_plane_restr0.005456
X-RAY DIFFRACTIONf_dihedral_angle_d2.781381
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1559-1.1690.43471530.37982876302980
1.169-1.18280.33171800.347936223802100
1.1828-1.19720.34941930.332536083801100
1.1972-1.21240.3451720.338336593831100
1.2124-1.22830.3421820.327936243806100
1.2283-1.24520.33651830.31636053788100
1.2452-1.26290.32482000.341636253825100
1.2629-1.28180.34892030.336836093812100
1.2818-1.30180.32941960.332936073803100
1.3018-1.32320.38241710.330836453816100
1.3232-1.3460.37981870.35313625381299
1.346-1.37050.41211930.3723596378999
1.3705-1.39680.43681740.40536113785100
1.3968-1.42530.46062100.511136333843100
1.4253-1.45630.58211840.589736713855100
1.4563-1.49020.28821970.327436083805100
1.4902-1.52750.27121780.277536733851100
1.5275-1.56880.25462090.243836363845100
1.5688-1.6150.28761730.224936843857100
1.615-1.66710.22042100.205736493859100
1.6671-1.72670.18741900.187736633853100
1.7267-1.79580.18881960.178936593855100
1.7958-1.87750.18241770.164937083885100
1.8775-1.97650.17641920.165737123904100
1.9765-2.10040.17311800.162436863866100
2.1004-2.26250.17882320.160336903922100
2.2625-2.49020.19211870.175737433930100
2.4902-2.85050.20191960.171837723968100
2.8505-3.59110.18822130.170438094022100
3.5911-46.56770.20222330.167340214254100
Refinement TLS params.Method: refined / Origin x: 11.4159 Å / Origin y: 30.4364 Å / Origin z: -2.5505 Å
111213212223313233
T0.1215 Å20.0098 Å20.0182 Å2-0.1309 Å2-0.0047 Å2--0.1264 Å2
L1.2017 °20.24 °20.58 °2-0.3002 °20.0985 °2--0.5776 °2
S0.0229 Å °0.0519 Å °-0.0385 Å °0.0016 Å °-0.0125 Å °0.0429 Å °0.0238 Å °-0.0194 Å °-0.0046 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 316
2X-RAY DIFFRACTION1allA400 - 964
3X-RAY DIFFRACTION1allA969 - 1083
4X-RAY DIFFRACTION1allA1085 - 1245
5X-RAY DIFFRACTION1allA1246 - 1400
6X-RAY DIFFRACTION1allB31 - 32

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