[English] 日本語
Yorodumi
- PDB-6iff: Crystal structure of M1 zinc metallopeptidase E323A mutant from D... -

+
Open data


ID or keywords:

Loading...

-
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


membrane alanyl aminopeptidase / metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more