[English] 日本語
Yorodumi
- PDB-6lh7: Crystal Structure of Vibrio cholerae Methionine Aminopeptidase wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lh7
TitleCrystal Structure of Vibrio cholerae Methionine Aminopeptidase with Partially Occupied Metals
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / peta-bread fold / metallo enzyme / MetAP
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / proteolysis / metal ion binding / cytosol
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like
Similarity search - Domain/homology
NICKEL (II) ION / Methionine aminopeptidase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.473 Å
AuthorsPillalamarri, V. / Addlagatta, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2015/000461 India
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Methionine aminopeptidases with short sequence inserts within the catalytic domain are differentially inhibited: Structural and biochemical studies of three proteins from Vibrio spp.
Authors: Pillalamarri, V. / Reddy, C.G. / Bala, S.C. / Jangam, A. / Kutty, V.V. / Addlagatta, A.
History
DepositionDec 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionine aminopeptidase
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,79612
Polymers67,1472
Non-polymers64910
Water9,908550
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0828
Polymers33,5731
Non-polymers5097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-23 kcal/mol
Surface area11910 Å2
MethodPISA
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7144
Polymers33,5731
Non-polymers1403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-23 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.702, 50.293, 131.684
Angle α, β, γ (deg.)90.000, 97.241, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Methionine aminopeptidase / MetAP / Peptidase M


Mass: 33573.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: map, VC_2261 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KPV1, methionyl aminopeptidase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 49.41 %
Description: Rhomboid shaped crystals are observed within 12 hours
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M Hepes pH-7.3 , 10% PEG 3350, 5% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9536 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.47→49.31 Å / Num. obs: 108944 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 17.6 / Num. measured all: 684923 / Scaling rejects: 38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.560.6763165852550.8410.2940.7392.797.7
8.07-49.315.60.02940327160.9990.0130.03246.698.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.503
Highest resolutionLowest resolution
Rotation48.18 Å1.67 Å

-
Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
MOLREPphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K26

6k26


Resolution: 1.473→48.226 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.016 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1765 5364 4.925 %
Rwork0.1518 --
all0.153 --
obs-108924 99.646 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.755 Å2-0 Å20.026 Å2
2--0.544 Å20 Å2
3---0.198 Å2
Refinement stepCycle: LAST / Resolution: 1.473→48.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 30 550 4958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134719
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174476
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.6446425
X-RAY DIFFRACTIONr_angle_other_deg1.511.57910461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05622.669251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78215880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7511531
X-RAY DIFFRACTIONr_chiral_restr0.0960.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025315
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02942
X-RAY DIFFRACTIONr_nbd_refined0.2250.2883
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24157
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22255
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2369
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1770.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.228
X-RAY DIFFRACTIONr_nbd_other0.1940.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.234
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3110.22
X-RAY DIFFRACTIONr_mcbond_it1.4671.4192306
X-RAY DIFFRACTIONr_mcbond_other1.4631.4182305
X-RAY DIFFRACTIONr_mcangle_it2.0692.1272899
X-RAY DIFFRACTIONr_mcangle_other2.0712.1282900
X-RAY DIFFRACTIONr_scbond_it2.8311.8042413
X-RAY DIFFRACTIONr_scbond_other2.8051.8032413
X-RAY DIFFRACTIONr_scangle_it4.262.573493
X-RAY DIFFRACTIONr_scangle_other4.2522.573493
X-RAY DIFFRACTIONr_lrange_it5.11318.3075316
X-RAY DIFFRACTIONr_lrange_other5.07217.8365189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.473-1.5110.233920.2197478X-RAY DIFFRACTION98.1419
1.511-1.5530.2253380.2027421X-RAY DIFFRACTION99.4616
1.553-1.5980.2213700.1847189X-RAY DIFFRACTION99.0046
1.598-1.6470.1813420.1677074X-RAY DIFFRACTION99.7847
1.647-1.7010.1943410.1656786X-RAY DIFFRACTION99.8599
1.701-1.7610.1853560.1546591X-RAY DIFFRACTION99.9712
1.761-1.8270.1843170.1496397X-RAY DIFFRACTION99.9851
1.827-1.9020.1753100.1446149X-RAY DIFFRACTION100
1.902-1.9860.1663420.1425888X-RAY DIFFRACTION99.9839
1.986-2.0830.1643020.1385617X-RAY DIFFRACTION99.9156
2.083-2.1960.1672790.145343X-RAY DIFFRACTION99.9111
2.196-2.3290.1632590.1325070X-RAY DIFFRACTION99.9625
2.329-2.490.1612560.1314804X-RAY DIFFRACTION99.9408
2.49-2.6890.1672350.1344410X-RAY DIFFRACTION99.957
2.689-2.9460.1732220.1454141X-RAY DIFFRACTION99.9084
2.946-3.2930.1482120.143696X-RAY DIFFRACTION99.9744
3.293-3.8020.1821700.153273X-RAY DIFFRACTION99.7104
3.802-4.6560.1551510.1412805X-RAY DIFFRACTION99.7974
4.656-6.580.2081100.1882180X-RAY DIFFRACTION99.7387
6.58-48.2260.256600.211248X-RAY DIFFRACTION98.941

+
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