[English] 日本語
Yorodumi
- PDB-2jjy: Crystal structure of Francisella tularensis enoyl reductase (ftFa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jjy
TitleCrystal structure of Francisella tularensis enoyl reductase (ftFabI) with bound NAD
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
KeywordsOXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesFRANCISELLA TULARENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLuckner, S.R. / Lu, H. / Truglio, J.J. / Tonge, P.J. / Kisker, C.
CitationJournal: Acs Chem.Biol. / Year: 2009
Title: Slow-Onset Inhibition of the Fabi Enoyl Reductase from Francisella Tularensis: Residence Time and in Vivo Activity
Authors: Lu, H. / England, K. / Am Ende, C. / Truglio, J.J. / Luckner, S.R. / Marlenee, N. / Knudson, S.E. / Knudson, D.L. / Bowen, R.A. / Kisker, C. / Slayden, R.A. / Tonge, P.J.
History
DepositionApr 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2895
Polymers115,6254
Non-polymers6631
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17020 Å2
ΔGint-102.6 kcal/mol
Surface area34400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.006, 99.454, 111.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 190
2114B2 - 190
3114C2 - 190
4114D2 - 190
1124A210 - 256
2124B210 - 256
3124C210 - 256
4124D210 - 256

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.3624, 0.7155, -0.5973), (0.7231, -0.1885, -0.6645), (-0.588, -0.6728, -0.4491)-15.96, 16.3, 2.61
2given(-0.7557, 0.2715, 0.5959), (0.2755, -0.6938, 0.6654), (0.5941, 0.6671, 0.4495)-39.14, -9.74, 20.67
3given(0.1312, -0.9913, 0.005114), (-0.9914, -0.1312, -0.000349), (0.001017, -0.005024, -1)-20.98, -23.96, 22.93
4given(-0.364, 0.7118, -0.6007), (0.7233, -0.1903, -0.6638), (-0.5868, -0.6761, -0.4456)-15.91, 16.25, 2.584
5given(-0.7534, 0.2738, 0.5978), (0.2762, -0.6933, 0.6656), (0.5967, 0.6666, 0.4467)-39.02, -9.81, 20.78
6given(0.1226, -0.9925, -0.001494), (-0.9925, -0.1226, -0.002326), (0.002125, 0.001768, -1)-21.01, -23.84, 23.09

-
Components

#1: Protein
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE / ENOYL REDUCTASE / NADH


Mass: 28906.348 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: 6XHISTIDINE AT C-TERMINUS / Source: (natural) FRANCISELLA TULARENSIS (bacteria)
References: UniProt: Q14I55, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.05 % / Description: NONE
Crystal growpH: 8 / Details: PEG 3350, MG ACETATE., pH 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.105
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2.9→36.32 Å / Num. obs: 24222 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019 24/04/2001refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→36.32 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.826 / SU B: 39.833 / SU ML: 0.345 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A194 - A204 DISORDERED; RESIDUES B196 - B211 DISORDERED; RESIDUES C193 - C207 DISORDERED; RESIDUES D193 - C204 DISORDERED; ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A194 - A204 DISORDERED; RESIDUES B196 - B211 DISORDERED; RESIDUES C193 - C207 DISORDERED; RESIDUES D193 - C204 DISORDERED; ADDITIONAL RESIDUES AT C- TERMINUS OF CHAIN A, B, C FROM 6XHISTIDINE TAG.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1231 5.12 %RANDOM
Rwork0.202 ---
obs0.206 24222 99.8 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 9.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.897 Å20 Å20 Å2
2--0.244 Å20 Å2
3----1.141 Å2
Refinement stepCycle: LAST / Resolution: 2.9→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7531 0 44 0 7575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227712
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.96210423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0285995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77624.625307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.868151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5721528
X-RAY DIFFRACTIONr_chiral_restr0.1050.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025687
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.23808
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25315
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4310.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4171.55057
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69727875
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.98532973
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5514.52547
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1417medium positional0.380.5
12B1417medium positional0.370.5
13C1417medium positional0.380.5
14D1417medium positional0.440.5
21A328medium positional0.340.5
22B328medium positional0.350.5
23C328medium positional0.410.5
24D328medium positional0.340.5
11A1417medium thermal0.512
12B1417medium thermal0.462
13C1417medium thermal0.492
14D1417medium thermal0.482
21A328medium thermal0.512
22B328medium thermal0.52
23C328medium thermal0.612
24D328medium thermal0.542
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 93 -
Rwork0.259 1620 -
obs--98.22 %
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)
10.9283-0.1175-0.89821.0792-0.67531.4539-0.06120.1954-0.1021-0.13610.0605-0.00830.068-0.00570.0007-0.09450.0229-0.0012-0.0605-0.0287-0.0779-1.515-6.1323-0.828
21.81740.0952-0.6451.5612-0.28640.9180.0238-0.08610.21210.17650.01150.0442-0.37930.0052-0.03530.00020.0238-0.0091-0.1097-0.0301-0.0771-20.271416.82086.474
31.34290.038-0.48211.5385-0.58561.1829-0.02290.2351-0.0511-0.13920.01450.13880.046-0.3380.0084-0.09290.0143-0.0345-0.0397-0.0173-0.0743-39.8863-6.222615.0483
41.65420.2353-0.60791.1673-0.52641.52820.0046-0.1067-0.1120.2146-0.0781-0.16730.03690.15570.0735-0.05810.0427-0.0143-0.10880.0001-0.0923-15.4058-22.688322.6828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 268
2X-RAY DIFFRACTION2B2 - 263
3X-RAY DIFFRACTION3C2 - 268
4X-RAY DIFFRACTION4D2 - 260

+
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://pdbjlvh1.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