[English] 日本語
Yorodumi
- PDB-3no9: Crystal Structure of apo fumarate hydratase from Mycobacterium tu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3no9
TitleCrystal Structure of apo fumarate hydratase from Mycobacterium tuberculosis
ComponentsFumarate hydratase class II
KeywordsLYASE / apo / Structural Genomics / TB Structural Genomics Consortium / fumarate hydratase / tricarboxylic acid cycle / lyase class I / TBSGC
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytosol
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fumarate hydratase class II / Fumarate hydratase class II
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLi, H. / Swanson, S. / Yu, M. / Hung, L.-W. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure of apo fumarate hydratase from Mycobacterium tuberculosis
Authors: Li, H. / Swanson, S. / Yu, M. / Hung, L.-H. / Sacchettini, J.S.
History
DepositionJun 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fumarate hydratase class II
B: Fumarate hydratase class II
C: Fumarate hydratase class II
D: Fumarate hydratase class II


Theoretical massNumber of molelcules
Total (without water)201,1164
Polymers201,1164
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25090 Å2
ΔGint-137 kcal/mol
Surface area57520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.224, 96.555, 89.889
Angle α, β, γ (deg.)90.00, 102.99, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 21:232 OR RESSEQ 241: 313 OR...
211CHAIN B AND (RESSEQ 21:232 OR RESSEQ 241: 313 OR...
311CHAIN C AND (RESSEQ 21:232 OR RESSEQ 241: 313 OR...
411CHAIN D AND (RESSEQ 21:232 OR RESSEQ 241: 313 OR...

-
Components

#1: Protein
Fumarate hydratase class II / Fumarase C


Mass: 50278.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fum, fumC, MT1130, MTV017.51c, Rv1098c / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53446, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 18% PEG 400, 0.1M sodium acetate pH 4.5, 0.2M calcium chloride, drop ratio 1:1, protein concentration 8mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2007
Details: VERTICALLY COLLIMATING PREMIRROR, LN2 COOLED DOUBLE- CRYSTAL SILICON (111) MONOCHROMATOR, TOROIDAL FOCUSING M2 MIRROR
RadiationMonochromator: LIQUID NITROGEN COOLED DUAL CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→48.523 Å / Num. obs: 70730 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 40.99 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 8.6
Reflection shellResolution: 2.48→2.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.39 / Rsym value: 0.414 / % possible all: 71.9

-
Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YFE

1yfe


Resolution: 2.48→48.52 Å / SU ML: 0.25 / σ(F): 1.91 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 3533 5 %
Rwork0.206 --
obs0.208 70709 88.4 %
all-70773 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.56 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4885 Å2-0 Å2-2.1327 Å2
2---5.8135 Å20 Å2
3---6.302 Å2
Refinement stepCycle: LAST / Resolution: 2.48→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13421 0 0 178 13599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813630
X-RAY DIFFRACTIONf_angle_d1.05818528
X-RAY DIFFRACTIONf_dihedral_angle_d14.3644958
X-RAY DIFFRACTIONf_chiral_restr0.0722214
X-RAY DIFFRACTIONf_plane_restr0.0042451
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2787X-RAY DIFFRACTIONPOSITIONAL
12B2787X-RAY DIFFRACTIONPOSITIONAL0.052
13C2787X-RAY DIFFRACTIONPOSITIONAL0.052
14D2787X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4826-2.51660.3138570.24981066X-RAY DIFFRACTION36
2.5166-2.55250.30731150.23872163X-RAY DIFFRACTION71
2.5525-2.59060.31531320.24972228X-RAY DIFFRACTION74
2.5906-2.63110.31221420.24042227X-RAY DIFFRACTION74
2.6311-2.67430.27611160.22992284X-RAY DIFFRACTION76
2.6743-2.72040.24681140.21852387X-RAY DIFFRACTION78
2.7204-2.76980.2761530.222428X-RAY DIFFRACTION81
2.7698-2.82310.24641140.22672460X-RAY DIFFRACTION81
2.8231-2.88070.29661100.21692583X-RAY DIFFRACTION84
2.8807-2.94330.24361360.222605X-RAY DIFFRACTION86
2.9433-3.01180.27471190.21072701X-RAY DIFFRACTION88
3.0118-3.08710.22871390.21382766X-RAY DIFFRACTION92
3.0871-3.17060.2641660.21922841X-RAY DIFFRACTION95
3.1706-3.26380.25041420.22192968X-RAY DIFFRACTION97
3.2638-3.36920.25261600.22563007X-RAY DIFFRACTION99
3.3692-3.48960.25961430.20443021X-RAY DIFFRACTION99
3.4896-3.62920.2411690.193014X-RAY DIFFRACTION99
3.6292-3.79430.21221530.1943047X-RAY DIFFRACTION100
3.7943-3.99430.20321610.17863035X-RAY DIFFRACTION100
3.9943-4.24440.2281620.17643044X-RAY DIFFRACTION100
4.2444-4.57190.20311900.16382983X-RAY DIFFRACTION100
4.5719-5.03160.20391730.1693048X-RAY DIFFRACTION99
5.0316-5.75860.21771550.19063058X-RAY DIFFRACTION100
5.7586-7.25140.23421350.21093096X-RAY DIFFRACTION100
7.2514-48.53260.26111770.23373116X-RAY DIFFRACTION99

+
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