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- PDB-1lml: LEISHMANOLYSIN -

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Basic information

Entry
Database: PDB / ID: 1lml
TitleLEISHMANOLYSIN
ComponentsLEISHMANOLYSIN
KeywordsLEISHMANOLYSIN / METALLOPROTEASE / GLYCOPROTEIN
Function / homology
Function and homology information


leishmanolysin / symbiont-mediated suppression of host JAK-STAT cascade / symbiont-mediated activation of host signal transduction pathway / symbiont-mediated suppression of host complement activation by inactivation of complement proteins / symbiont-mediated perturbation of host inflammatory response / side of membrane / metalloendopeptidase activity / metallopeptidase activity / cell adhesion / proteolysis ...leishmanolysin / symbiont-mediated suppression of host JAK-STAT cascade / symbiont-mediated activation of host signal transduction pathway / symbiont-mediated suppression of host complement activation by inactivation of complement proteins / symbiont-mediated perturbation of host inflammatory response / side of membrane / metalloendopeptidase activity / metallopeptidase activity / cell adhesion / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Leishmanolysin; domain 3 / Leishmanolysin domain 3 / Leishmanolysin; domain 4 / Leishmanolysin domain 4 / Elastase; domain 1 - #20 / Leishmanolysin; domain 2 / Leishmanolysin , domain 2 / Peptidase M8, leishmanolysin / Leishmanolysin / Elastase; domain 1 ...Leishmanolysin; domain 3 / Leishmanolysin domain 3 / Leishmanolysin; domain 4 / Leishmanolysin domain 4 / Elastase; domain 1 - #20 / Leishmanolysin; domain 2 / Leishmanolysin , domain 2 / Peptidase M8, leishmanolysin / Leishmanolysin / Elastase; domain 1 / Ribbon / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MOLECULAR REPLACEMENT USING TWO CRYSTAL FORMS / Resolution: 1.86 Å
AuthorsSchlagenhauf, E. / Etges, R. / Metcalf, P.
Citation
Journal: Structure / Year: 1998
Title: The crystal structure of the Leishmania major surface proteinase leishmanolysin (gp63).
Authors: Schlagenhauf, E. / Etges, R. / Metcalf, P.
#1: Journal: Thesis
Title: X-Ray Crystallographic Studies of Leishmanolysin the Leishmania Major Surface Metalloproteinase from Leishmania Major
Authors: Schlagenhauf, E.
#2: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Leishmanolysin, the Major Surface Metalloproteinase from Leishmania Major
Authors: Schlagenhauf, E. / Etges, R. / Metcalf, P.
History
DepositionMar 13, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEISHMANOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6732
Polymers51,6081
Non-polymers651
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.325, 90.144, 70.145
Angle α, β, γ (deg.)90.00, 110.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LEISHMANOLYSIN / GP63 PROTEIN / PSP


Mass: 51607.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / Cellular location: MEMBRANE BOUND / Strain: LRC-L119 / References: UniProt: P08148, leishmanolysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 59.65 %
Crystal growMethod: vapor diffusion - hanging drop -macroseeding / pH: 9.5
Details: 52% MPD (2-METHYL-2,4-PENTANEDIOL) 0.1M ETHANOLAMINE-HCL PH 9.5 0.02% NA-AZIDE VAPOR DIFFUSION HANGING DROP METHOD WITH MACROSEEDING, vapor diffusion - hanging drop -macroseeding
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
248-50 %satammonium sulfate1reservoir
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.86→40 Å / Num. obs: 51879 / % possible obs: 99.7 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 6.1
Reflection shellResolution: 1.86→1.94 Å / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.2 / % possible all: 99.3
Reflection
*PLUS
% possible obs: 99.5 % / Redundancy: 5.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT USING TWO CRYSTAL FORMS
Resolution: 1.86→5 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: UNINTERPRETABLE WEAK ELECTRON DENSITY WAS OBSERVED FOR RESIDUES 408 - 412, 499 - 504, 575 - 577 AND FOR THE CARBOHYDRATE CHAINS ATTACHED TO N 300, N 407, N 534, N 577.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 4626 9.5 %RANDOM
Rwork0.191 ---
obs0.191 48665 98.7 %-
Displacement parametersBiso mean: 24.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.86→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 1 212 3806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.98
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.611.5
X-RAY DIFFRACTIONx_mcangle_it2.72
X-RAY DIFFRACTIONx_scbond_it2.762
X-RAY DIFFRACTIONx_scangle_it4.342.5
LS refinement shellResolution: 1.86→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 823 10.3 %
Rwork0.244 7189 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19_HOH.SOL
X-RAY DIFFRACTION3PARAM.ZINC
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.195 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.98
LS refinement shell
*PLUS
Lowest resolution: 1.94 Å / Rfactor Rfree: 0.272 / % reflection Rfree: 10 % / Rfactor obs: 0.258

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