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- PDB-6iff: Crystal structure of M1 zinc metallopeptidase E323A mutant from D... -

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Basic information

Entry
Database: PDB / ID: 6iff
TitleCrystal structure of M1 zinc metallopeptidase E323A mutant from Deinococcus radiodurans
ComponentsZinc 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
TYROSINE / Aminopeptidase N
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsAgrawal, R. / Kumar, A. / Kumar, A. / Gaur, N.K. / 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
DepositionSep 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: 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 1.2Apr 7, 2021Group: Derived calculations / Category: struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._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 1.3Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,6358
Polymers103,0962
Non-polymers5396
Water7,855436
1
A: Zinc metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8174
Polymers51,5481
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area16530 Å2
MethodPISA
2
B: Zinc metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8174
Polymers51,5481
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.480, 57.658, 69.786
Angle α, β, γ (deg.)89.66, 82.07, 67.54
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: 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-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / 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.: 436 / 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: 1.88 Å3/Da / Density % sol: 34.54 % / Description: Plate like crystal
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5 / Details: 0.2M ammonium formate, 0.1M Bis-tris, 20% PEG 3350 / PH range: 5.0-7.0

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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 27, 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: 1.83→45.36 Å / Num. obs: 64195 / % possible obs: 97.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 8.397 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.053 / Rrim(I) all: 0.084 / Net I/σ(I): 12.2
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3730 / CC1/2: 0.657 / Rpim(I) all: 0.415 / Rrim(I) all: 0.645 / % possible all: 89.9

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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: 1.83→22.265 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.67
RfactorNum. reflection% reflection
Rfree0.215 3091 4.82 %
Rwork0.1832 --
obs0.1847 64131 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→22.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 0 30 436 7076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056822
X-RAY DIFFRACTIONf_angle_d0.7569338
X-RAY DIFFRACTIONf_dihedral_angle_d12.1714042
X-RAY DIFFRACTIONf_chiral_restr0.0471058
X-RAY DIFFRACTIONf_plane_restr0.0061220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.85860.37161350.322547X-RAY DIFFRACTION88
1.8586-1.88910.31371350.25042716X-RAY DIFFRACTION96
1.8891-1.92160.30031400.23332773X-RAY DIFFRACTION97
1.9216-1.95650.28381490.22562706X-RAY DIFFRACTION97
1.9565-1.99420.26731360.21652801X-RAY DIFFRACTION97
1.9942-2.03480.20321500.21292744X-RAY DIFFRACTION97
2.0348-2.0790.24971410.19622764X-RAY DIFFRACTION97
2.079-2.12740.2381460.19192745X-RAY DIFFRACTION97
2.1274-2.18050.23041310.1922821X-RAY DIFFRACTION97
2.1805-2.23940.23771360.1812743X-RAY DIFFRACTION97
2.2394-2.30530.2111150.18222818X-RAY DIFFRACTION97
2.3053-2.37960.22041470.18242787X-RAY DIFFRACTION98
2.3796-2.46450.21491240.18482782X-RAY DIFFRACTION98
2.4645-2.56310.23661370.18932809X-RAY DIFFRACTION98
2.5631-2.67950.24021610.19272784X-RAY DIFFRACTION98
2.6795-2.82050.22311530.19532790X-RAY DIFFRACTION98
2.8205-2.99690.20811200.20262813X-RAY DIFFRACTION98
2.9969-3.22760.27561260.19652852X-RAY DIFFRACTION99
3.2276-3.55130.20051440.18192807X-RAY DIFFRACTION99
3.5513-4.06240.17851430.1562845X-RAY DIFFRACTION99
4.0624-5.1080.14541610.12372797X-RAY DIFFRACTION99
5.108-22.26620.15321610.14482796X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -41.5789 Å / Origin y: -41.0229 Å / Origin z: 6.007 Å
111213212223313233
T0.1457 Å2-0.0012 Å2-0.0056 Å2-0.1346 Å2-0.012 Å2--0.1472 Å2
L0.0649 °20.0479 °2-0.0348 °2-0.1978 °2-0.1593 °2--0.2745 °2
S0.0064 Å °0.0199 Å °0.0082 Å °-0.0233 Å °-0.0034 Å °0.0069 Å °-0.0241 Å °0.0087 Å °-0.0015 Å °
Refinement TLS groupSelection details: all

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