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- PDB-1ge5: ZINC PEPTIDASE FROM GRIFOLA FRONDOSA -

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Basic information

Entry
Database: PDB / ID: 1ge5
TitleZINC PEPTIDASE FROM GRIFOLA FRONDOSA
ComponentsPEPTIDYL-LYS METALLOENDOPEPTIDASE
KeywordsHYDROLASE / zinc coordinate / METALLOPROTEASE
Function / homology
Function and homology information


peptidyl-Lys metalloendopeptidase / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Lysine-specific metallo-endopeptidase / Peptidyl-Lys metallopeptidase catalytic domain / Lysine-specific metallo-endopeptidase / Lysine-specific metallo-endopeptidase / : / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Peptidyl-Lys metalloendopeptidase
Similarity search - Component
Biological speciesGrifola frondosa (maitake)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHori, T. / Kumasaka, T. / Yamamoto, M. / Nonaka, T. / Tanaka, N. / Hashimoto, Y. / Ueki, T. / Takio, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.
Authors: Hori, T. / Kumasaka, T. / Yamamoto, M. / Nonaka, N. / Tanaka, N. / Hashimoto, Y. / Ueki, U. / Takio, K.
History
DepositionOct 11, 2000Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDYL-LYS METALLOENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3043
Polymers18,0581
Non-polymers2462
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.800, 40.500, 30.500
Angle α, β, γ (deg.)105.90, 91.70, 103.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PEPTIDYL-LYS METALLOENDOPEPTIDASE


Mass: 18058.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Grifola frondosa (maitake) / Tissue: FRUITING BODY
References: UniProt: P81054, peptidyl-Lys metalloendopeptidase
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 293 K / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMacetate1drop
30.1-3.0 M1reservoirNaCl
410 mMimidazole1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 15, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29.8 Å / Num. all: 17364 / Num. obs: 6440 / % possible obs: 64.8 % / Observed criterion σ(F): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 5.4
Reflection shellResolution: 2.25→3 Å / Rmerge(I) obs: 0.199 / Num. unique all: 1262 / % possible all: 43.4
Reflection
*PLUS
Num. all: 9943 / Num. measured all: 17364
Reflection shell
*PLUS
% possible obs: 43.4 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
AMoREphasing
CNSrefinement
PROCESS(RIGAKU)data scaling
RefinementResolution: 2→29.8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 328 -RANDOM
Rwork0.184 ---
all-9115 --
obs-6440 64.8 %-
Refinement stepCycle: LAST / Resolution: 2→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 12 131 1407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.16
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 29.8 Å / % reflection Rfree: 5 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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