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- PDB-6a8z: Crystal structure of M1 zinc metallopeptidase from Deinococcus ra... -

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Basic information

Entry
Database: PDB / ID: 6a8z
TitleCrystal structure of M1 zinc metallopeptidase from Deinococcus radiodurans
ComponentsZinc metalloprotease, putative
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: 2.045 Å
AuthorsAgrawal, R. / 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
DepositionJul 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 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_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

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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)103,7518
Polymers103,2122
Non-polymers5396
Water6,161342
1
A: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8754
Polymers51,6061
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area16840 Å2
MethodPISA
2
B: Zinc metalloprotease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8754
Polymers51,6061
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.371, 57.583, 69.579
Angle α, β, γ (deg.)89.74, 82.30, 67.53
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Zinc metalloprotease, putative


Mass: 51605.828 Da / Num. of mol.: 2
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 / Details: Tyrosine as ligand / 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.: 342 / 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: 1.97 Å3/Da / Density % sol: 33.85 % / Description: plate like crystal
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 0.23M Ammonium formate, 27% PEG3350
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: 0.979476 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2017 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979476 Å / Relative weight: 1
ReflectionResolution: 2.045→45.3 Å / Num. obs: 45670 / % possible obs: 97.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.249 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 14.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3200 / CC1/2: 0.843 / Rpim(I) all: 0.267 / Rrim(I) all: 0.467 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
PHENIXmodel building
MR-Rosettaphasing
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H19

1h19


Resolution: 2.045→30.251 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 2243 4.91 %
Rwork0.175 --
obs0.1772 45644 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.045→30.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6639 0 30 342 7011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076857
X-RAY DIFFRACTIONf_angle_d0.9059392
X-RAY DIFFRACTIONf_dihedral_angle_d3.7394813
X-RAY DIFFRACTIONf_chiral_restr0.0541065
X-RAY DIFFRACTIONf_plane_restr0.0061229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0454-2.08990.26721150.24212392X-RAY DIFFRACTION86
2.0899-2.13850.29381320.20562715X-RAY DIFFRACTION97
2.1385-2.19190.23511490.20752686X-RAY DIFFRACTION97
2.1919-2.25120.23951600.19642697X-RAY DIFFRACTION97
2.2512-2.31740.27681450.18892717X-RAY DIFFRACTION97
2.3174-2.39220.26931330.19392730X-RAY DIFFRACTION97
2.3922-2.47760.23411230.18752719X-RAY DIFFRACTION97
2.4776-2.57680.27171500.18782731X-RAY DIFFRACTION98
2.5768-2.6940.24131480.19482721X-RAY DIFFRACTION98
2.694-2.83590.26581420.19662715X-RAY DIFFRACTION98
2.8359-3.01340.23461210.2022779X-RAY DIFFRACTION98
3.0134-3.24590.27071280.19622771X-RAY DIFFRACTION99
3.2459-3.5720.2091430.17532738X-RAY DIFFRACTION99
3.572-4.08780.18091390.14932800X-RAY DIFFRACTION99
4.0878-5.14610.16921520.12542748X-RAY DIFFRACTION99
5.1461-30.25430.15561630.13912742X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3065-0.09660.08851.1413-0.07790.22640.0191-0.01520.0447-0.0633-0.00880.0135-0.0157-0.0169-0.01380.159-0.01240.00770.1648-0.01130.1457-49.1216-52.260523.4193
20.63820.0362-0.09411.35830.20020.69860.04870.0407-0.06030.0031-0.0469-0.08040.00110.0419-0.0050.1828-0.0174-0.02560.17350.01150.127-33.8465-29.1887-12.3933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 36:471)
2X-RAY DIFFRACTION2(chain B and resseq 36:468)

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