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- PDB-6koy: Crystal structure of two domain M1 Zinc metallopeptidase E323A mu... -

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Basic information

Entry
Database: PDB / ID: 6koy
TitleCrystal structure of two domain M1 Zinc metallopeptidase E323A mutant bound to L-tryptophan amino acid
ComponentsZinc metalloproteaseMetalloproteinase
KeywordsHYDROLASE / Metalloprotease
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily
Similarity search - Domain/homology
TRYPTOPHAN / Aminopeptidase N
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsAgrawal, R. / Kumar, A. / Kumar, A. / Makde, R.D.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural basis for the unusual substrate specificity of unique two-domain M1 metallopeptidase.
Authors: Agrawal, R. / Goyal, V.D. / Singh, R. / Kumar, A. / Jamdar, S.N. / Kumar, A. / Makde, R.D.
History
DepositionAug 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc metalloprotease
B: Zinc metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6356
Polymers103,0962
Non-polymers5394
Water5,981332
1
A: Zinc metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8173
Polymers51,5481
Non-polymers2702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zinc metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8173
Polymers51,5481
Non-polymers2702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.833, 57.457, 69.492
Angle α, β, γ (deg.)89.754, 82.636, 67.928
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLY(chain 'A' and (resid 36 through 85 or (resid 86...AA36 - 23338 - 235
12GLUGLUVALVAL(chain 'A' and (resid 36 through 85 or (resid 86...AA236 - 277238 - 279
13ASPASPGLUGLU(chain 'A' and (resid 36 through 85 or (resid 86...AA280 - 466282 - 468
21GLNGLNGLYGLY(chain 'B' and ((resid 36 and (name N or name...BB36 - 23338 - 235
22GLUGLUVALVAL(chain 'B' and ((resid 36 and (name N or name...BB236 - 277238 - 279
23ASPASPGLUGLU(chain 'B' and ((resid 36 and (name N or name...BB280 - 466282 - 468

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Components

#1: Protein Zinc metalloprotease / Metalloproteinase / M1 zinc metallopeptidase


Mass: 51547.793 Da / Num. of mol.: 2 / Mutation: E323A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0875 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9RVZ5
#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.25 % / Description: Plate like crystals
Crystal growTemperature: 294 K / Method: microbatch / Details: Bis-Tris, ammonium formate, PEG3350 / PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9794 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 7, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.35→44.89 Å / Num. obs: 29930 / % possible obs: 97.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 24.45 Å2 / CC1/2: 0.996 / Net I/σ(I): 14.3
Reflection shellResolution: 2.35→2.43 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2663 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6a8z

6a8z


Resolution: 2.35→41.91 Å / SU ML: 0.2821 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.7301
RfactorNum. reflection% reflection
Rfree0.2215 1450 4.85 %
Rwork0.1658 --
obs0.1685 29913 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.37 Å2
Refinement stepCycle: LAST / Resolution: 2.35→41.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 32 332 6892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00376752
X-RAY DIFFRACTIONf_angle_d0.67859269
X-RAY DIFFRACTIONf_chiral_restr0.04531062
X-RAY DIFFRACTIONf_plane_restr0.00511209
X-RAY DIFFRACTIONf_dihedral_angle_d2.94435405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.35-2.430.28591100.2186261989.48
2.43-2.530.30051420.1887284697.94
2.53-2.650.29781640.1831284797.89
2.65-2.790.26511570.1758285698.14
2.79-2.960.23061240.1752289098.34
2.96-3.190.24681330.1791289798.66
3.19-3.510.18391410.1643288298.73
3.51-4.020.21571470.1489287398.82
4.02-5.060.19491650.1412287799.15
5.060.1821670.1626287699.12

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