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- PDB-6ifg: Crystal structure of M1 zinc metallopeptidase E323A mutant bound ... -

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Basic information

Entry
Database: PDB / ID: 6ifg
TitleCrystal structure of M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala substrate from Deinococcus radiodurans
Components
  • Tripeptides (TYR-SER-ALA)
  • Zinc metalloprotease
KeywordsHYDROLASE / Metalloprotease / peptidase
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
FORMIC ACID / Aminopeptidase N
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
Deinococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAgrawal, R. / Kumar, A. / Kumar, A. / Makde, R.D.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Two-domain aminopeptidase of M1 family: Structural features for substrate binding and gating in absence of C-terminal domain.
Authors: Agrawal, R. / Goyal, V.D. / Kumar, A. / Gaur, N.K. / Jamdar, S.N. / Kumar, A. / Makde, R.D.
History
DepositionSep 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
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
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
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_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.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.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_conn.ptnr2_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
B: Zinc metalloprotease
E: Tripeptides (TYR-SER-ALA)
F: Tripeptides (TYR-SER-ALA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,63421
Polymers103,7744
Non-polymers86017
Water4,576254
1
A: Zinc metalloprotease
E: Tripeptides (TYR-SER-ALA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,34011
Polymers51,8872
Non-polymers4539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-42 kcal/mol
Surface area16490 Å2
MethodPISA
2
B: Zinc metalloprotease
F: Tripeptides (TYR-SER-ALA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,29410
Polymers51,8872
Non-polymers4078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-43 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.598, 57.594, 69.321
Angle α, β, γ (deg.)89.77, 82.14, 67.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Zinc metalloprotease / 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 / Plasmid: pST50TR / Details (production host): pET3a based / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9RVZ5
#2: Protein/peptide Tripeptides (TYR-SER-ALA)


Mass: 339.345 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide substrate sequence is designed and synthesized based on the enzymatic assay of the M1 metallopeptidase from Deinococcus radiodurans
Source: (synth.) Deinococcus (bacteria)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.84 Å3/Da / Density % sol: 33.03 % / Description: Plate like crystals
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5
Details: 0.2M Ammonium formate, 0.1M Bis-tris pH 5.5, 25% PEG 3350
PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 28, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.9→44.83 Å / Num. obs: 56301 / % possible obs: 97.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 13.046 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.039 / Rrim(I) all: 0.065 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3603 / CC1/2: 0.865 / Rpim(I) all: 0.269 / Rrim(I) all: 0.446 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A8Z

6a8z


Resolution: 1.9→24.137 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.61
RfactorNum. reflection% reflection
Rfree0.2142 2750 4.89 %
Rwork0.1805 --
obs0.1821 56240 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 43 255 6956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056858
X-RAY DIFFRACTIONf_angle_d0.7969370
X-RAY DIFFRACTIONf_dihedral_angle_d13.0434043
X-RAY DIFFRACTIONf_chiral_restr0.051063
X-RAY DIFFRACTIONf_plane_restr0.0051224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93280.27081360.24042665X-RAY DIFFRACTION96
1.9328-1.96790.2521440.21562636X-RAY DIFFRACTION96
1.9679-2.00570.2551420.20572619X-RAY DIFFRACTION97
2.0057-2.04670.25011430.2052667X-RAY DIFFRACTION97
2.0467-2.09110.22091290.19752625X-RAY DIFFRACTION97
2.0911-2.13980.22821330.18992693X-RAY DIFFRACTION97
2.1398-2.19320.231440.19042625X-RAY DIFFRACTION97
2.1932-2.25250.2311650.17822630X-RAY DIFFRACTION97
2.2525-2.31870.22431250.18772699X-RAY DIFFRACTION97
2.3187-2.39350.22931150.1872659X-RAY DIFFRACTION97
2.3935-2.4790.23971240.19182706X-RAY DIFFRACTION98
2.479-2.57810.24951540.19342683X-RAY DIFFRACTION98
2.5781-2.69530.23881400.19422671X-RAY DIFFRACTION98
2.6953-2.83720.25691350.18932673X-RAY DIFFRACTION98
2.8372-3.01460.22461140.19332739X-RAY DIFFRACTION98
3.0146-3.24690.24311260.19162705X-RAY DIFFRACTION99
3.2469-3.57270.18721430.17022702X-RAY DIFFRACTION99
3.5727-4.08750.1761310.16182739X-RAY DIFFRACTION99
4.0875-5.14160.16711520.14492685X-RAY DIFFRACTION99
5.1416-24.13880.18271550.16112669X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -41.9149 Å / Origin y: -40.7837 Å / Origin z: 5.5599 Å
111213212223313233
T0.1319 Å2-0.0098 Å2-0.0023 Å2-0.1558 Å2-0.0109 Å2--0.1674 Å2
L0.0984 °20.0685 °2-0.0264 °2-0.2677 °2-0.1747 °2--0.4146 °2
S-0.0118 Å °0.0174 Å °0.0053 Å °-0.0269 Å °0.0136 Å °0.0013 Å °-0.0136 Å °-0.0041 Å °-0.0007 Å °
Refinement TLS groupSelection details: all

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