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- PDB-6kp0: Crystal structure of two domain M1 zinc metallopeptidase E323A mu... -

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Basic information

Entry
Database: PDB / ID: 6kp0
TitleCrystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-arginine
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
ARGININE / Aminopeptidase N
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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_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
A: Zinc metalloprotease, putative
B: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6238
Polymers103,0962
Non-polymers5276
Water2,648147
1
A: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8114
Polymers51,5481
Non-polymers2643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area16320 Å2
MethodPISA
2
B: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8114
Polymers51,5481
Non-polymers2643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.632, 57.204, 67.049
Angle α, β, γ (deg.)89.860, 85.080, 68.570
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 36 through 207 or (resid 208...
21(chain B and ((resid 36 and (name N or name...

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
11GLNGLNTHRTHR(chain A and (resid 36 through 207 or (resid 208...AA36 - 20738 - 209
12GLUGLUARGARG(chain A and (resid 36 through 207 or (resid 208...AA208 - 209210 - 211
13GLNGLNVALVAL(chain A and (resid 36 through 207 or (resid 208...AA36 - 46838 - 470
14GLNGLNVALVAL(chain A and (resid 36 through 207 or (resid 208...AA36 - 46838 - 470
15GLNGLNVALVAL(chain A and (resid 36 through 207 or (resid 208...AA36 - 46838 - 470
16GLNGLNVALVAL(chain A and (resid 36 through 207 or (resid 208...AA36 - 46838 - 470
21GLNGLNGLNGLN(chain B and ((resid 36 and (name N or name...BB3638
22GLNGLNVALVAL(chain B and ((resid 36 and (name N or name...BB36 - 46838 - 470
23GLNGLNVALVAL(chain B and ((resid 36 and (name N or name...BB36 - 46838 - 470
24GLNGLNVALVAL(chain B and ((resid 36 and (name N or name...BB36 - 46838 - 470
25GLNGLNVALVAL(chain B and ((resid 36 and (name N or name...BB36 - 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-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / 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.: 147 / 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: 1.75 Å3/Da / Density % sol: 29.56 %
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: Dec 3, 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: 2.1→46.94 Å / Num. obs: 39796 / % possible obs: 97.8 % / Redundancy: 3.9 % / CC1/2: 0.998 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 3180 / CC1/2: 0.92

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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: 2.1→33.385 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.05
RfactorNum. reflection% reflection
Rfree0.2638 1924 4.84 %
Rwork0.2306 --
obs0.2322 39767 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.68 Å2 / Biso mean: 28.1504 Å2 / Biso min: 11.69 Å2
Refinement stepCycle: final / Resolution: 2.1→33.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 28 148 6746
Biso mean--52.7 25.95 -
Num. residues----865
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2638X-RAY DIFFRACTION3.893TORSIONAL
12B2638X-RAY DIFFRACTION3.893TORSIONAL
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 (%)
2.1001-2.15260.29141260.2726262897
2.1526-2.21080.33271400.257270697
2.2108-2.27580.29441310.2597266497
2.2758-2.34920.30431440.265271397
2.3492-2.43320.28471180.2491272797
2.4332-2.53060.29261530.258267098
2.5306-2.64570.33861530.2633269098
2.6457-2.78510.28431310.2642271398
2.7851-2.95950.2791110.2664271998
2.9595-3.18780.32461270.2606275098
3.1878-3.50830.27061390.2319271998
3.5083-4.01530.25081400.2025272399
4.0153-5.0560.19891510.1822271599
5.0560.2191600.1914270699
Refinement TLS params.Method: refined / Origin x: 30.1543 Å / Origin y: 13.1391 Å / Origin z: 6.0575 Å
111213212223313233
T0.1285 Å2-0.0188 Å20.0001 Å2-0.1319 Å2-0.0118 Å2--0.1848 Å2
L0.0773 °20.1266 °2-0.1031 °2-0.6926 °2-0.2904 °2--0.7508 °2
S-0.0267 Å °0.0072 Å °0.0047 Å °-0.0346 Å °-0.002 Å °0.0043 Å °-0.0327 Å °0.0503 Å °0.0264 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA36 - 468
2X-RAY DIFFRACTION1allB36 - 468
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD2 - 3
5X-RAY DIFFRACTION1allE1 - 150
6X-RAY DIFFRACTION1allF1 - 2

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