[English] 日本語
Yorodumi
- PDB-3h5h: LeuD_1-186 small subunit of isopropylmalate isomerase (Rv2987c) f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h5h
TitleLeuD_1-186 small subunit of isopropylmalate isomerase (Rv2987c) from mycobacterium tuberculosis
Components3-isopropylmalate dehydratase small subunit
KeywordsLYASE / Leucine biosynthesis / isopropylmalate isomerase / LeuD / M.tuberculosis / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis
Function / homology
Function and homology information


3-isopropylmalate dehydratase complex / 3-isopropylmalate dehydratase / 3-isopropylmalate dehydratase activity / L-leucine biosynthetic process / plasma membrane
Similarity search - Function
3-isopropylmalate dehydratase, small subunit / 3-isopropylmalate dehydratase, swivel domain / : / Aconitase; domain 4 / Aconitase, domain 4 / Aconitase A/isopropylmalate dehydratase small subunit, swivel domain / Aconitase C-terminal domain / Aconitase/3-isopropylmalate dehydratase, swivel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-isopropylmalate dehydratase small subunit / 3-isopropylmalate dehydratase small subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsManikandan, K. / Geerlof, A. / Weiss, M.S.
Citation
Journal: Proteins / Year: 2011
Title: Structural studies on the enzyme complex isopropylmalate isomerase (LeuCD) from Mycobacterium tuberculosis
Authors: Manikandan, K. / Geerlof, A. / Zozulya, A.V. / Svergun, D.I. / Weiss, M.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the small subunit of isopropylmalate isomerase (Rv2987c) from Mycobacterium tuberculosis
Authors: Manikandan, K. / Geerlof, A. / Schuldt, L. / Mueller-Dieckmann, C. / Weiss, M.S.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-isopropylmalate dehydratase small subunit
B: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)41,2652
Polymers41,2652
Non-polymers00
Water70339
1
A: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)20,6321
Polymers20,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)20,6321
Polymers20,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.480, 70.290, 59.650
Angle α, β, γ (deg.)90.00, 124.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-187-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISPHEPHEAA5 - 298 - 32
21HISHISPHEPHEBB5 - 298 - 32
12ARGARGLEULEUAA35 - 16738 - 170
22ARGARGLEULEUBB35 - 16738 - 170
DetailsAS THE STRUCTURE REPRESENTS ONLY A PART OF A SUBUNIT OF AN ENZYME COMPLEX, THE ASSEMBLIES DESCRIBED IN REMARK350 IS NOT RELEVANT TO THE REAL BIOLOGICAL ASSEMBLIES

-
Components

#1: Protein 3-isopropylmalate dehydratase small subunit / Isopropylmalate isomerase small subunit / Alpha-IPM isomerase / IPMI


Mass: 20632.318 Da / Num. of mol.: 2 / Fragment: LeuD, residues 1-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2987c / Plasmid: pETM11 / Production host: Escherichia coli (E. coli)
References: UniProt: P65277, UniProt: P9WK95*PLUS, 3-isopropylmalate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SER 1A WAS INTRODUCED WHILE CLONING.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M NaCl, 0.1M Hepes pH 7.0, 1.2M Ammonium sulphate, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2008
RadiationMonochromator: Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→51 Å / Num. all: 10727 / Num. obs: 10727 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.2 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5E

3h5e


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.843 / SU B: 13.29 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26863 518 4.8 %RANDOM
Rwork0.2257 ---
obs0.22788 10185 99.04 %-
all-10727 --
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: 19 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-1.22 Å2
2---1.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 0 39 2632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9443597
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0765333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41122.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9515411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3081523
X-RAY DIFFRACTIONr_chiral_restr0.070.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212037
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5531.51655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1032.52651
X-RAY DIFFRACTIONr_scbond_it2.3985992
X-RAY DIFFRACTIONr_scangle_it4.05910946
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A632tight positional0.050.05
2B587medium positional0.040.5
1A632tight thermal0.251.5
2B587medium thermal0.412.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 29 -
Rwork0.241 708 -
obs--93.77 %

+
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