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- PDB-6kp1: Crystal structure of two domain M1 zinc metallopeptidase E323A mu... -

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Basic information

Entry
Database: PDB / ID: 6kp1
TitleCrystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-methionine 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
METHIONINE / Aminopeptidase N
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Zinc metalloprotease, putative
B: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5718
Polymers103,0962
Non-polymers4756
Water7,152397
1
A: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7854
Polymers51,5481
Non-polymers2383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area16220 Å2
MethodPISA
2
B: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7854
Polymers51,5481
Non-polymers2383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.806, 57.496, 69.444
Angle α, β, γ (deg.)89.921, 82.483, 67.829
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 36 through 106 or (resid 107...A36 - 277
121(chain 'A' and (resid 36 through 106 or (resid 107...A280 - 467
211(chain 'B' and (resid 36 through 235 or (resid 236...B36 - 277
221(chain 'B' and (resid 36 through 235 or (resid 236...B280 - 467
112chain 'E'E1
212chain 'F'F1

NCS ensembles :
ID
1
2

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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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 1.84 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: 0.9778 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.19→47.5 Å / Num. obs: 36707 / % possible obs: 97.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.55 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.6
Reflection shellResolution: 2.19→2.26 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2953 / CC1/2: 0.956

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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: 2.19→21.45 Å / SU ML: 0.2724 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 29.727
RfactorNum. reflection% reflection
Rfree0.2702 1772 4.84 %
Rwork0.2179 --
obs0.2204 36649 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.26 Å2
Refinement stepCycle: LAST / Resolution: 2.19→21.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 22 397 7002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256778
X-RAY DIFFRACTIONf_angle_d0.61619292
X-RAY DIFFRACTIONf_chiral_restr0.04081062
X-RAY DIFFRACTIONf_plane_restr0.00441216
X-RAY DIFFRACTIONf_dihedral_angle_d2.86724731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.32321300.25662477X-RAY DIFFRACTION89.4
2.25-2.320.28591320.23992665X-RAY DIFFRACTION97.05
2.32-2.390.34861230.24392684X-RAY DIFFRACTION97.16
2.39-2.480.30671260.23582709X-RAY DIFFRACTION97.59
2.48-2.580.32561500.24242685X-RAY DIFFRACTION97.49
2.58-2.690.31351420.24042681X-RAY DIFFRACTION97.92
2.69-2.840.32171460.23262688X-RAY DIFFRACTION97.99
2.84-3.010.28491150.2422752X-RAY DIFFRACTION98.15
3.01-3.240.31781250.22772728X-RAY DIFFRACTION98.18
3.24-3.570.22591430.20982687X-RAY DIFFRACTION98.5
3.57-4.080.21751330.18962755X-RAY DIFFRACTION98.94
4.08-5.130.24131520.17972703X-RAY DIFFRACTION98.99
5.13-21.450.22671550.21142663X-RAY DIFFRACTION97.54

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