[English] 日本語
Yorodumi
- PDB-6j72: Crystal structure of IniA from Mycobacterium smegmatis with GTP bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j72
TitleCrystal structure of IniA from Mycobacterium smegmatis with GTP bound
ComponentsIsoniazid inducible gene protein IniA
KeywordsHYDROLASE / GTPase / dynamin-like / drug-resistance
Function / homology
Function and homology information


GTP binding / metal ion binding / membrane
Similarity search - Function
: / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / L(+)-TARTARIC ACID / Isoniazid inducible gene protein IniA
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsWang, M.F. / Guo, X.Y. / Hu, J.J. / Li, J. / Rao, Z.H.
Funding support China, 10items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020200 China
Ministry of Science and Technology (China)2016YFA0500201 China
Ministry of Science and Technology (China)2017YFC0840300 China
Ministry of Science and Technology (China)2014CB542800 China
Ministry of Science and Technology (China)2014CBA02003 China
National Natural Science Foundation of China813300237 China
National Natural Science Foundation of China81520108019 China
National Natural Science Foundation of China31630020 China
National Natural Science Foundation of China31500607 China
Chinese Academy of SciencesXDPB10 China
CitationJournal: Nat Commun / Year: 2019
Title: Mycobacterial dynamin-like protein IniA mediates membrane fission.
Authors: Wang, M. / Guo, X. / Yang, X. / Zhang, B. / Ren, J. / Liu, A. / Ran, Y. / Yan, B. / Chen, F. / Guddat, L.W. / Hu, J. / Li, J. / Rao, Z.
History
DepositionJan 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoniazid inducible gene protein IniA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2834
Polymers66,5861
Non-polymers6983
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-14 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.514, 91.514, 139.494
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein Isoniazid inducible gene protein IniA


Mass: 66585.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: iniA, MSMEI_0678 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FE16
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: AAA

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 33615 / % possible obs: 100 % / Redundancy: 20.6 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.03 / Rrim(I) all: 0.134 / Χ2: 0.724 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2421.20.53916700.9580.120.5520.457100
2.24-2.2820.90.47216680.9580.1060.4830.478100
2.28-2.3220.70.43416660.9670.0970.4440.482100
2.32-2.3720.50.3816800.9750.0860.390.49100
2.37-2.4220.20.34516750.9780.0790.3540.506100
2.42-2.4819.10.30716870.9810.0720.3150.504100
2.48-2.5419.50.27416720.9830.0640.2820.531100
2.54-2.6120.90.25216680.9870.0560.2580.555100
2.61-2.6921.30.22416830.9890.050.2290.569100
2.69-2.7721.30.21216760.990.0470.2170.585100
2.77-2.8721.10.17916740.9920.040.1840.648100
2.87-2.9921.10.16216720.9930.0360.1660.678100
2.99-3.1220.50.14616670.9940.0330.150.721100
3.12-3.2919.20.1316960.9950.030.1340.782100
3.29-3.49210.12116810.9960.0270.1240.883100
3.49-3.7621.60.11416660.9970.0250.1170.982100
3.76-4.1421.20.10616960.9970.0240.1091.101100
4.14-4.7419.50.09916870.9970.0230.1021.12899.9
4.74-5.9720.90.10416990.9960.0240.1071.071100
5.97-5020.10.09317320.9960.0220.0961.305100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.498 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.33
RfactorNum. reflection% reflection
Rfree0.2211 1690 5.04 %
Rwork0.1847 --
obs0.1865 33560 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.27 Å2 / Biso mean: 48.9126 Å2 / Biso min: 20.97 Å2
Refinement stepCycle: final / Resolution: 2.2→46.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4335 0 43 333 4711
Biso mean--51.93 48.19 -
Num. residues----561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044450
X-RAY DIFFRACTIONf_angle_d0.8446038
X-RAY DIFFRACTIONf_chiral_restr0.032699
X-RAY DIFFRACTIONf_plane_restr0.004797
X-RAY DIFFRACTIONf_dihedral_angle_d16.5631675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.26350.24531780.2299256399
2.2635-2.33660.2551500.21472625100
2.3366-2.42010.27791500.21562672100
2.4201-2.5170.23721330.21452642100
2.517-2.63150.28411120.21132682100
2.6315-2.77020.26321140.22132694100
2.7702-2.94380.24581450.21392645100
2.9438-3.1710.26441350.20692661100
3.171-3.490.24461550.19792640100
3.49-3.99480.22921370.17212679100
3.9948-5.03210.1781470.14342664100
5.0321-46.4980.15781340.15732703100
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)
11.79820.9490.26332.7025-1.87716.1936-0.102-0.0708-0.11980.10060.07890.19920.3993-0.60430.04180.41330.07440.00920.40860.0240.5517-15.84747.833845.1186
21.477-0.06150.08461.77530.93192.03670.17940.049-0.3862-0.09440.16870.56320.3343-0.6831-0.26550.3970.02180.00060.3990.11850.3371-1.579816.051746.985
30.95880.07590.25251.8283-0.6583.54360.0636-0.0914-0.19030.15450.080.11670.0414-0.2763-0.15810.29490.03380.00860.24950.04460.25134.122918.58846.2275
40.9945-1.98431.36174.853-2.05931.6374-0.1073-0.20230.20340.304-0.0216-0.1782-0.1053-0.29290.10440.44070.11390.08250.42080.02180.367-4.692340.690353.6464
52.7719-2.8158-0.26144.27760.72460.73780.0050.07090.09990.0739-0.0556-0.0836-0.072-0.02790.01680.29950.06580.02460.1840.01720.254913.747338.111530.5897
60.44880.10350.10580.23040.57271.068-0.15990.06130.25940.15380.3599-0.48080.06890.126-0.25910.4573-0.02970.06760.4362-0.01220.536113.752222.170727.858
73.2715-3.3965-0.24925.03330.82690.86080.25890.2648-0.166-0.358-0.24030.1425-0.0708-0.02370.02110.33980.08080.03940.25850.02630.2888.762333.898626.5897
83.1515-0.80190.53654.5966-1.19482.0189-0.3797-0.44250.54570.66970.3530.3197-0.9527-0.75370.08880.65070.26620.04020.5794-0.08110.5821-18.123666.344248.588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 33 )A-1 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 78 )A34 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 241 )A79 - 241
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 298 )A242 - 298
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 409 )A299 - 409
6X-RAY DIFFRACTION6chain 'A' and (resid 410 through 494 )A410 - 494
7X-RAY DIFFRACTION7chain 'A' and (resid 495 through 563 )A495 - 563
8X-RAY DIFFRACTION8chain 'A' and (resid 564 through 594 )A564 - 594

+
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