[English] 日本語
Yorodumi
- PDB-1rq2: MYCOBACTERIUM TUBERCULOSIS FTSZ IN COMPLEX WITH CITRATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rq2
TitleMYCOBACTERIUM TUBERCULOSIS FTSZ IN COMPLEX WITH CITRATE
ComponentsCell division protein ftsZ
KeywordsCELL CYCLE / SIGNALING PROTEIN / TUBULIN / GTPASE
Function / homology
Function and homology information


septin ring assembly / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / positive regulation of cell cycle / cell division / GTPase activity / GTP binding / magnesium ion binding ...septin ring assembly / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / positive regulation of cell cycle / cell division / GTPase activity / GTP binding / magnesium ion binding / plasma membrane / cytoplasm
Similarity search - Function
Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; ...Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Cell division protein FtsZ / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLeung, A.K.W. / White, E.L. / Ross, L.J. / Reynolds, R.C. / DeVito, J.A. / Borhani, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structure of Mycobacterium tuberculosis FtsZ reveals unexpected, G protein-like conformational switches.
Authors: Leung, A.K. / Lucile White, E. / Ross, L.J. / Reynolds, R.C. / DeVito, J.A. / Borhani, D.W.
#1: Journal: To be Published
Title: Polymerization of C-Terminally Truncated Mycobacterium tuberculosis FtsZ Is Unlikely to be Physiologically Relevant
Authors: Borhani, D.W. / White, E.L.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization of the Mycobacterium tuberculosis cell-division protein FtsZ
Authors: Leung, A.K.W. / White, E.L. / Ross, L.J. / Borhani, D.W.
#3: Journal: J.Bacteriol. / Year: 2000
Title: Slow polymerization of Mycobacterium tuberculosis FtsZ
Authors: White, E.L. / Ross, L.J. / Reynolds, R.C. / Seitz, L.E. / Moore, G.D. / Borhani, D.W.
#4: Journal: J.ANTIMICROB.CHEMOTHER. / Year: 2002
Title: 2-Alkoxycarbonylaminopyridines: inhibitors of Mycobacterium tuberculosis FtsZ
Authors: White, E.L. / Suling, W.J. / Ross, L.J. / Seitz, L.E. / Reynolds, R.C.
History
DepositionDec 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division protein ftsZ
B: Cell division protein ftsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3383
Polymers78,1462
Non-polymers1921
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-5 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.116, 88.116, 176.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Cell division protein ftsZ


Mass: 39073.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: FTSZ, RV2150C, MT2209, MTCY270.18, MB2174C / Plasmid: pJD168 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: P64170, UniProt: P9WN95*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.58 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 30% PEG 4000, 0.1M SODIUM CITRATE, 0.2M AMMONIUM ACETATE, 2MM SRI-7614, ETHYL (6-AMINO-2,3-DIHYDRO-4-PHENYL-1H-PYRIDO[4,3-B][1,4]DIAZEPIN-8-YL)-CARBAMATE, WAS INCLUDED AS WELL, BUT WAS NOT ...Details: 30% PEG 4000, 0.1M SODIUM CITRATE, 0.2M AMMONIUM ACETATE, 2MM SRI-7614, ETHYL (6-AMINO-2,3-DIHYDRO-4-PHENYL-1H-PYRIDO[4,3-B][1,4]DIAZEPIN-8-YL)-CARBAMATE, WAS INCLUDED AS WELL, BUT WAS NOT LOCATED IN THE FINAL STRUCTURE, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9235
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 30, 2000 / Details: MIRRORS/MONOCHROMATOR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9235 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. obs: 68271 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.68 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.4
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.409 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
EPMRphasing
REFMAC5.1.27refinement
X-PLORrefinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FSZ

1fsz


Resolution: 1.86→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.621 / SU ML: 0.079 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: X-PLOR-GENERATED BULK SOLVENT PARTIAL STRUCTURE FACTORS WERE USED IN REFMAC AS PARTIAL STRUCTURE FACTORS (FPART/PHIPART), EXCEPT IN LAST ROUND, WHERE REFMAC BABINET MODEL WITH MASK WAS USED. ...Details: X-PLOR-GENERATED BULK SOLVENT PARTIAL STRUCTURE FACTORS WERE USED IN REFMAC AS PARTIAL STRUCTURE FACTORS (FPART/PHIPART), EXCEPT IN LAST ROUND, WHERE REFMAC BABINET MODEL WITH MASK WAS USED. AFTER COMPLETION OF THE REFINEMENT, AN UNINTERPRETABLE STRETCH OF ELECTRON DENSITY REMAINED NEAR THE ACTIVE SITE OF SUBUNIT A. THIS DENSITY IS DISTINCT FROM THE CITRATE (AND SURROUNDING WATER MOLECULES) IN THE ACTIVE SITE. NONE OF THE OTHER CRYSTALLIZATION BUFFER COMPONENTS COULD BE MODELED INTO THIS DENSITY. A THREE OR FOUR RESIDUE PEPTIDE COULD BE MODELED INTO THIS DENSITY, BUT NOT IN A VERY SATISFACTORY MANNER. THE DENSITY MAY ARISE FROM PARTIAL ORDERING OF THE AMINO-TERMINUS OF ANOTHER FTSZ MOLECULE IN THE CRYSTAL LATTICE, OR MORE LIKELY FROM ONE OF THE PEPTIDIC PROTEASE INHIBITORS INCLUDED IN THE PROTEIN PREPARATION (E.G., LEUPEPTIN).
RfactorNum. reflection% reflectionSelection details
Rfree0.22169 3267 5.1 %RANDOM
Rwork0.18707 ---
obs0.18887 61177 99.17 %-
all-64447 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.217 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.86→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 13 316 4600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9815827
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023178
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.22212
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2331
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0641.52904
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97524628
X-RAY DIFFRACTIONr_scbond_it3.19931410
X-RAY DIFFRACTIONr_scangle_it5.7344.51199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 243
Rwork0.26 4518

+
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