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- PDB-4q1l: Crystal structure of Leucurolysin-a complexed with an endogenous ... -

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Basic information

Entry
Database: PDB / ID: 4q1l
TitleCrystal structure of Leucurolysin-a complexed with an endogenous tripeptide (QSW).
Components
  • GLN-SER-TRP
  • Snake venom metalloproteinase leucurolysin-A
KeywordsHYDROLASE / Alfa/Beta Protein / Metalloendopeptidase / Zinc Binding Calcium Binding / Venom Compound
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / fibrinolysis / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region / plasma membrane
Similarity search - Function
Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Snake venom metalloproteinase leucurolysin-A
Similarity search - Component
Biological speciesBothrops leucurus (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFerreira, R.N. / Sanchez, E.O.F. / Pimenta, A.M.C. / Nagem, R.A.P.
Citation
Journal: To be Published
Title: Crystal structure of Leucurolysin-a complexed with an endogenous tripeptide (QSW).
Authors: Ferreira, R.N. / Rates, B. / Richardson, M. / Guimaraes, B.G. / Sanchez, E.O.F. / Pimenta, A.M.C. / Nagem, R.A.P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Complete amino-acid sequence, crystallization and preliminary X-ray diffraction studies of leucurolysin-a, a nonhaemorrhagic metalloproteinase from Bothrops leucurus snake venom.
Authors: Ferreira, R.N. / Rates, B. / Richardson, M. / Guimaraes, B.G. / Sanchez, E.O. / Pimenta, A.M. / Nagem, R.A.
History
DepositionApr 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...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 / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Snake venom metalloproteinase leucurolysin-A
D: GLN-SER-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6826
Polymers23,4562
Non-polymers2274
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-48 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.350, 58.408, 76.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#1: Protein Snake venom metalloproteinase leucurolysin-A / Leuc-A / SVMP


Mass: 23036.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Venom compound / Source: (natural) Bothrops leucurus (snake)
References: UniProt: P84907, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide GLN-SER-TRP


Mass: 419.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Venom compound / Source: (natural) Bothrops leucurus (snake)

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Non-polymers , 5 types, 214 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsAUTHORS HAVE INDICATED THAT THE THE SEQUENCE 102-VAL:103-PHE IN THE PDB FILE IS THE CORRECT ONE AS ...AUTHORS HAVE INDICATED THAT THE THE SEQUENCE 102-VAL:103-PHE IN THE PDB FILE IS THE CORRECT ONE AS SUPPORTED BY THE ELECTRON DENSITY. THE SEQUENCE 102-PHE:103-LEU IS INCORRECT. AUTHORS HAVE INDICATED THAT IT IS MORE LIKELY THAT THE SEQUENCE, OBTAINED BY EDMAN DEGRADATION, WAS NOT CORRECT AT THIS PART OF THE PROTEIN.

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 6000, 0.1 M MIB/MIB 0.1 M AMMONIUM ACETATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.425 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2010 / Details: MIRRORS
RadiationMonochromator: CURVED CRYSTAL OF SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 16359 / Num. obs: 16352 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-1.971100
1.97-4.091100
4.09-50199.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERCrystallographic Software 2.5.3phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GBO

3gbo


Resolution: 1.9→32.099 Å / SU ML: 0.18 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 822 5.04 %
Rwork0.1535 --
obs0.1554 16304 99.86 %
all-16327 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→32.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 10 210 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081731
X-RAY DIFFRACTIONf_angle_d1.2352344
X-RAY DIFFRACTIONf_dihedral_angle_d13.697646
X-RAY DIFFRACTIONf_chiral_restr0.078258
X-RAY DIFFRACTIONf_plane_restr0.005305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8993-2.01830.21131370.16592521X-RAY DIFFRACTION99
2.0183-2.17410.20561430.15012509X-RAY DIFFRACTION100
2.1741-2.39280.21831470.15332550X-RAY DIFFRACTION100
2.3928-2.73890.21361420.14822555X-RAY DIFFRACTION100
2.7389-3.45010.16721220.14562623X-RAY DIFFRACTION100
3.4501-32.10350.17511310.15952724X-RAY DIFFRACTION100

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