[English] 日本語
Yorodumi
- PDB-6t77: Crystal structure of Klebsiella pneumoniae FabG(NADPH-dependent) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t77
TitleCrystal structure of Klebsiella pneumoniae FabG(NADPH-dependent) NADP-complex at 1.75 A resolution
Components3-oxoacyl-ACP reductase
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / NADPH / complex / FAS-II
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / NAD binding / fatty acid biosynthetic process
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVella, P. / Schnell, R. / Lindqvist, Y. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Vinnova Sweden
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: A FabG inhibitor targeting an allosteric binding site inhibits several orthologs from Gram-negative ESKAPE pathogens.
Authors: Vella, P. / Rudraraju, R.S. / Lundback, T. / Axelsson, H. / Almqvist, H. / Vallin, M. / Schneider, G. / Schnell, R.
History
DepositionOct 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Refinement description
Category: citation / citation_author / pdbx_refine_tls_group
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7334
Polymers51,2462
Non-polymers1,4872
Water3,909217
1
A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
hetero molecules

A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The same tetrameric arrangement is observed as for many FabG enzymes from various bacteria. The asymmetric unit contains a dimer (chains A,B), the tetramer is formed by the ...Evidence: gel filtration, The same tetrameric arrangement is observed as for many FabG enzymes from various bacteria. The asymmetric unit contains a dimer (chains A,B), the tetramer is formed by the dimerization of this dimer.
  • 105 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)105,4678
Polymers102,4934
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area17020 Å2
ΔGint-83 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.723, 118.842, 119.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 244 / Label seq-ID: 2 - 245

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein 3-oxoacyl-ACP reductase / 3-oxoacyl-ACP reductase FabG / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier- ...3-oxoacyl-ACP reductase FabG / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase FabG / Beta-ketoacyl-ACP reductase / FabG protein


Mass: 25623.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was expressed in E.coli with N-terminal His6-tag (removable by TEV protease cleavage). The tag removal results in a protein with one extra Serine residue at the N-terminus.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: fabG, fabG_1, fabG_10, fabG_11, fabG_13, fabG_17, fabG_2, fabG_20, fabG_29, fabG_3, fabG_5, fabG_6, fabG_7, fabG_9, B4U21_08660, B4U25_10170, B4U30_10945, BANRA_00187, BANRA_00827, BL124_ ...Gene: fabG, fabG_1, fabG_10, fabG_11, fabG_13, fabG_17, fabG_2, fabG_20, fabG_29, fabG_3, fabG_5, fabG_6, fabG_7, fabG_9, B4U21_08660, B4U25_10170, B4U30_10945, BANRA_00187, BANRA_00827, BL124_00014385, BN49_2178, BU230_37105, BVX91_09955, C1459_07275, C3483_16280, C3F39_04320, C4Y50_026525, C7V41_16750, C8P71_1985, CSC88_11955, CWN54_18865, DD581_15755, DD583_12070, DM059_09455, DN589_06290, DXF97_11560, E0760_18120, EAO17_24465, EXT45_09615, FAQ72_04165, FAQ97_22680, FAS39_22705, NCTC11679_03520, NCTC13465_02289, NCTC13635_06738, NCTC1936_03302, NCTC204_06212, NCTC5052_01093, NCTC8849_02353, NCTC9128_07518, NCTC9178_04075, NCTC9617_01456, NCTC9637_04333, NCTC9645_00460, PMK1_03430, SAMEA104305404_12205, SAMEA104567806_03967, SAMEA104567857_00497, SAMEA104567903_00037, SAMEA23986918_09908, SAMEA3531848_01000, SAMEA4364603_00036, SAMEA4394730_07307, SAMEA4873640_04565, SK89_00756, SM87_01800
Plasmid: pNIC28Bsa4
Details (production host): N-terminal His6-tag (removable by TEV protease cleavage)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W9B6I8, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
Details: In chain A it is partialy disordered, and only the Pho-Adenine nucleotide segment is resolved in the electron density map.
Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 9.5 mg/ml protein solution mixed with NADP+ at 11.5 mM concentration Well solution: 0.1 M phosphate-citrate 4.2 pH 40 %v/v PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2017 / Details: Toroidal mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.75→59.88 Å / Num. obs: 47966 / % possible obs: 96.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.026 / Net I/σ(I): 15
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / Num. unique obs: 2647 / CC1/2: 0.861 / Rpim(I) all: 0.297 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q7B

1q7b


Resolution: 1.75→59.88 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 2449 5.1 %RANDOM
Rwork0.1579 ---
obs0.1596 45483 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.71 Å2 / Biso mean: 38.978 Å2 / Biso min: 21.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å2-0 Å2
2---1.82 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.75→59.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 75 217 3860
Biso mean--45.91 42.42 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193753
X-RAY DIFFRACTIONr_bond_other_d00.023586
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9885093
X-RAY DIFFRACTIONr_angle_other_deg3.73838270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33123.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6831530
X-RAY DIFFRACTIONr_chiral_restr0.1090.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024221
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02753
Refine LS restraints NCS

Ens-ID: 1 / Number: 14464 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 176 -
Rwork0.236 3418 -
all-3594 -
obs--99.06 %
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)
10.38260.3472-0.3161.26970.19221.10450.04170.01020.05340.2015-0.00840.07310.1939-0.1817-0.03320.1164-0.0459-0.05970.08180.01240.1082-13.092-20.117-21.44
20.84610.60050.09261.5185-0.11871.03910.0955-0.11840.15780.3216-0.01510.1541-0.1331-0.077-0.08050.09410.02760.02830.0513-0.02620.0448-8.75810.155-16.89
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 244
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B301

+
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