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- PDB-1eb6: Deuterolysin from Aspergillus oryzae -

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Basic information

Entry
Database: PDB / ID: 1eb6
TitleDeuterolysin from Aspergillus oryzae
ComponentsNEUTRAL PROTEASE II
KeywordsHYDROLASE / METALLOPROTEINASE / ZINC / NEUTRAL PROTEASE II
Function / homology
Function and homology information


deuterolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M35, deuterolysin / Deuterolysin metalloprotease (M35) family / : / 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
Biological speciesASPERGILLUS ORYZAE (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1 Å
AuthorsMcAuley, K.E. / Jia-Xing, Y. / Dodson, E.J. / Lehmbeck, J. / Ostergaard, P.R. / Wilson, K.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: A Quick Solution: Ab Initio Structure Determination of a 19 kDa Metalloproteinase Using Acorn
Authors: Mcauley, K.E. / Jia-Xing, Y. / Dodson, E.J. / Lehmbeck, J. / Ostergaard, P.R. / Wilson, K.S.
History
DepositionJul 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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.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.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: NEUTRAL PROTEASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2835
Polymers19,0321
Non-polymers2524
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.430, 34.764, 60.276
Angle α, β, γ (deg.)90.00, 106.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NEUTRAL PROTEASE II / NPII / DEUTEROLYSIN


Mass: 19031.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ASPERGILLUS ORYZAE (mold) / References: UniProt: P46076, deuterolysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERMOSTABLE METALLOPROTEASE. SHOWS HIGH ACTIVITIES FOR BASIC NUCLEAR SUBSTRATES.
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 Å3/Da / Density % sol: 39 %
Crystal growpH: 7.5 / Details: 1.8M NA,K PHOSPHATE, 0.1M HEPES PH 7.5
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
21.8 Msodium potassium phosphate1reservoir
30.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1→30 Å / Num. obs: 82199 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23
Reflection shellResolution: 1→1.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
DENZOdata reduction
SCALEPACKdata scaling
ACORNphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1→57.73 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.22 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.126 2439 3 %RANDOM
Rwork0.104 ---
obs-78791 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 1→57.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 13 259 1607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211429
X-RAY DIFFRACTIONr_bond_other_d0.0030.021149
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.3991.9671943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg4.15232737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1460.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021611
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02256
X-RAY DIFFRACTIONr_nbd_refined0.5230.3372
X-RAY DIFFRACTIONr_nbd_other0.330.31214
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.9780.521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.5193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.140.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.534
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6631.5884
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.50521426
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5883539
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0384.5504
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 186
Rwork0.199 5780
Software
*PLUS
Name: REFMAC / Version: 5.0.36 18/01/2001 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.103 / Rfactor Rfree: 0.126 / Rfactor Rwork: 0.104
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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