[English] 日本語
Yorodumi
- PDB-2yw9: Crystal structure of TT0143 from Thermus thermophilus HB8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yw9
TitleCrystal structure of TT0143 from Thermus thermophilus HB8
ComponentsEnoyl-[acyl carrier protein] reductase
KeywordsOXIDOREDUCTASE / Alpha and beta proteins (a/b) / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMiyano, M. / Ago, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of TT0143 from Thermus thermophilus HB8
Authors: Ago, H. / Hamada, K. / Ida, K. / Kanda, H. / Sugahara, M. / Yamamoto, M. / Nodake, Y. / Kuramitsu, S. / Yokoyama, S. / Miyano, M.
History
DepositionApr 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_ncs_dom_lim / struct_site
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.end_auth_comp_id / _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
E: Enoyl-[acyl carrier protein] reductase
F: Enoyl-[acyl carrier protein] reductase
G: Enoyl-[acyl carrier protein] reductase
H: Enoyl-[acyl carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,61810
Polymers225,1318
Non-polymers1,4872
Water6,954386
1
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)113,3095
Polymers112,5664
Non-polymers7431
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16890 Å2
ΔGint-105 kcal/mol
Surface area30250 Å2
MethodPISA, PQS
2
E: Enoyl-[acyl carrier protein] reductase
F: Enoyl-[acyl carrier protein] reductase
G: Enoyl-[acyl carrier protein] reductase
H: Enoyl-[acyl carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3095
Polymers112,5664
Non-polymers7431
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16920 Å2
ΔGint-110 kcal/mol
Surface area30420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.087, 107.131, 184.704
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
41E
51F
61G
71A
81B
91C
101E
111F
121G
12D
22H
32D
42H

NCS domain segments:

End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUAA2 - 1912 - 191
211LEULEUBB2 - 1912 - 191
311LEULEUCC2 - 1912 - 191
411LEULEUEE2 - 1912 - 191
511LEULEUFF2 - 1912 - 191
611LEULEUGG2 - 1912 - 191
721ALAALAAA212 - 256212 - 256
821ALAALABB212 - 256212 - 256
921ALAALACC212 - 256212 - 256
1021ALAALAEE212 - 256212 - 256
1121ALAALAFF212 - 256212 - 256
1221ALAALAGG212 - 256212 - 256
112LEULEUDD2 - 1912 - 191
212LEULEUHH2 - 1912 - 191
322ALAALADD212 - 256212 - 256
422ALAALAHH212 - 256212 - 256

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Enoyl-[acyl carrier protein] reductase


Mass: 28141.432 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLI9, EC: 1.3.1.10
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, LiCl, Sodium Citerate, NaCl, NADP(+), pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 29, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.5→38.876 Å / Num. obs: 66626 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 39.37 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 4.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.4 / Num. unique all: 9522 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.3.0027refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ULU

1ulu


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.961 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 2.765 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: NADPs at the binding site of enzyme with segment ID, A, B, C, E, F and G were not included in the model, due to the poor electron densities of them.
RfactorNum. reflection% reflectionSelection details
Rfree0.26273 6738 10.1 %RANDOM
Rwork0.22228 ---
obs0.22644 66487 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å20 Å2
2---2.73 Å20 Å2
3---4.95 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14247 0 96 386 14729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214635
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.961.99119952
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.52651974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92223.176507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.325152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7091587
X-RAY DIFFRACTIONr_chiral_restr0.0630.22388
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210917
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.17243
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.210260
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.182
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7051.59952
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.188215322
X-RAY DIFFRACTIONr_scbond_it1.94935281
X-RAY DIFFRACTIONr_scangle_it2.9634.54624
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
11A938tight positional0.060.05
11B938tight positional0.060
11C938tight positional0.040
11E938tight positional0.060
11F938tight positional0.040
11G938tight positional0.050
22D939tight positional0.040.05
11A705medium positional0.180.5
11B705medium positional0.180
11C705medium positional0.070
11E705medium positional0.10
11F705medium positional0.080
11G705medium positional0.080
22H717medium positional0.110.5
11A938tight thermal0.140.5
11B938tight thermal0.130
11C938tight thermal0.120
11E938tight thermal0.140
11F938tight thermal0.120
11G938tight thermal0.130
22D939tight thermal0.140.5
11A705medium thermal0.152
11B705medium thermal0.140
11C705medium thermal0.140
11E705medium thermal0.160
11F705medium thermal0.130
11G705medium thermal0.140
22H717medium thermal0.172
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 501 -
Rwork0.28 4288 -
obs--100 %

+
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