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- PDB-6koz: Crystal structure of two domain M1 zinc metallopeptidase E323 mut... -

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Basic information

Entry
Database: PDB / ID: 6koz
TitleCrystal structure of two domain M1 zinc metallopeptidase E323 mutant bound to L-Leucine amino acid
ComponentsZinc metalloprotease, putative
KeywordsHYDROLASE / Metalloprotease
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / metallopeptidase activity / proteolysis / zinc ion binding / cytoplasm
Similarity search - Function
Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / 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
LEUCINE / Aminopeptidase N
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,5358
Polymers103,0962
Non-polymers4396
Water6,810378
1
B: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7674
Polymers51,5481
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7674
Polymers51,5481
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.208, 57.420, 69.006
Angle α, β, γ (deg.)89.970, 82.760, 67.820
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 36 through 106 or (resid 107...
21(chain B and (resid 36 through 104 or (resid 105...

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
11GLNGLNVALVAL(chain A and (resid 36 through 106 or (resid 107...AB36 - 10638 - 108
12ARGARGARGARG(chain A and (resid 36 through 106 or (resid 107...AB107109
13GLNGLNPROPRO(chain A and (resid 36 through 106 or (resid 107...AB36 - 47138 - 473
14GLNGLNPROPRO(chain A and (resid 36 through 106 or (resid 107...AB36 - 47138 - 473
15GLNGLNPROPRO(chain A and (resid 36 through 106 or (resid 107...AB36 - 47138 - 473
16GLNGLNPROPRO(chain A and (resid 36 through 106 or (resid 107...AB36 - 47138 - 473
21GLNGLNGLNGLN(chain B and (resid 36 through 104 or (resid 105...BA36 - 10438 - 106
22ARGARGARGARG(chain B and (resid 36 through 104 or (resid 105...BA105107
23GLNGLNVALVAL(chain B and (resid 36 through 104 or (resid 105...BA36 - 46838 - 470
24GLNGLNVALVAL(chain B and (resid 36 through 104 or (resid 105...BA36 - 46838 - 470
25GLNGLNVALVAL(chain B and (resid 36 through 104 or (resid 105...BA36 - 46838 - 470
26GLNGLNVALVAL(chain B and (resid 36 through 104 or (resid 105...BA36 - 46838 - 470

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Components

#1: Protein Zinc metalloprotease, putative


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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 1.81 Å3/Da / Density % sol: 32 % / Description: plate like crystal
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: Aug 4, 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: 2.25→46.98 Å / Num. obs: 33608 / % possible obs: 98.2 % / Redundancy: 2.7 % / CC1/2: 0.994 / Net I/σ(I): 10.2
Reflection shellResolution: 2.25→2.32 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3066 / CC1/2: 0.883

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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: 2.25→26.551 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.38
RfactorNum. reflection% reflection
Rfree0.2723 1650 4.92 %
Rwork0.2182 --
obs0.2208 33542 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.73 Å2 / Biso mean: 27.5127 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 2.25→26.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6611 0 22 386 7019
Biso mean--22.97 27.85 -
Num. residues----869
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2638X-RAY DIFFRACTION3.692TORSIONAL
12B2638X-RAY DIFFRACTION3.692TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.31620.33291530.2909260097
2.3162-2.39090.37671210.273263397
2.3909-2.47630.32641300.2681266697
2.4763-2.57540.32381510.2564262798
2.5754-2.69250.3481430.2539266098
2.6925-2.83430.3371330.2494263498
2.8343-3.01160.28831210.254273198
3.0116-3.24380.32251230.2276265799
3.2438-3.56950.23771460.2055267899
3.5695-4.08440.2291260.1843269799
4.0844-5.13980.21311500.17267099
5.13980.22591530.1893263998

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