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- PDB-1ge7: ZINC PEPTIDASE FROM GRIFOLA FRONDOSA -

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Basic information

Entry
Database: PDB / ID: 1ge7
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 / SYNCHROTRON / 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-LYS METALLOENDOPEPTIDASE
B: PEPTIDYL-LYS METALLOENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6086
Polymers36,1172
Non-polymers4914
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.202, 30.202, 308.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein PEPTIDYL-LYS METALLOENDOPEPTIDASE


Mass: 18058.424 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 1.94 Å3/Da / Density % sol: 36.74 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.01
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2→38.3 Å / Num. all: 173122 / Num. obs: 137781 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.341 / Num. unique all: 1761 / % possible all: 98.1
Reflection
*PLUS
Num. obs: 18300 / Num. measured all: 137781
Reflection shell
*PLUS
% possible obs: 98.1 % / Mean I/σ(I) obs: 6.1

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
AMoREphasing
CNSrefinement
PROCESS(RIGAKU)data scaling
RefinementResolution: 2→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 928 -RANDOM
Rwork0.179 ---
all-173122 --
obs-18278 99 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 24 297 2863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.08
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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