[English] 日本語
Yorodumi
- PDB-7fcm: Crystal structure of Moraxella catarrhalis enoyl-ACP-reductase (F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fcm
TitleCrystal structure of Moraxella catarrhalis enoyl-ACP-reductase (FabI) in complex with NAD and Triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / FabI / NADH / Triclosan
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsKatiki, M. / Neetu, N. / Pratap, S. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BIC/12(29)/2013 India
Citation
Journal: Biochimie / Year: 2022
Title: Biochemical and structural basis for Moraxella catarrhalis enoyl-acyl carrier protein reductase (FabI) inhibition by triclosan and estradiol.
Authors: Katiki, M. / Neetu, N. / Pratap, S. / Kumar, P.
#1: Journal: To Be Published
Title: Crystal structure of Apo enoyl-ACP-reductase (FabI) from Moraxella catarrhalis
Authors: Katiki, M. / Pratap, S. / Kumar, P.
#2: Journal: To Be Published
Title: Crystal structure of enoyl-ACP-reductase (FabI) from Moraxella catarrhalis in complex with the cofactor NAD
Authors: Katiki, M. / Neetu, N. / Pratap, S. / Kumar, P.
History
DepositionJul 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Jan 31, 2024Group: Database references / Category: citation
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6747
Polymers61,7282
Non-polymers1,9465
Water3,333185
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,34814
Polymers123,4564
Non-polymers3,89210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area23150 Å2
ΔGint-229 kcal/mol
Surface area33390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.520, 78.560, 89.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: -1 - 265 / Label seq-ID: 12 - 278

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

-
Components

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


Mass: 30864.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (strain BBH18) (bacteria)
Gene: fabI, MCR_1078 / Plasmid: pET28C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D5VCE0, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.14 Å3/Da / Density % sol: 42.62 % / Description: Rod shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M calcium chloride, 0.1M HEPES buffer, 22% PEG 400, 10-folds of NADH cofactor, triclosan inhibitor

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 26533 / % possible obs: 97.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.067 / Rrim(I) all: 0.138 / Χ2: 1.889 / Net I/σ(I): 8.3 / Num. measured all: 100946
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.21-2.252.10.5536850.6570.4160.6971.17451
2.25-2.293.30.47613340.6570.2980.5651.20599.3
2.29-2.333.50.62813240.7240.3790.7371.106100
2.33-2.383.70.52613490.7540.3110.6141.11299.9
2.38-2.433.80.52513480.8160.3050.611.109100
2.43-2.493.90.45513200.8460.260.5271.102100
2.49-2.553.90.42913560.8790.2420.4951.213100
2.55-2.6240.35513510.8970.1970.4091.219100
2.62-2.740.30313400.9250.1670.3471.375100
2.7-2.7840.27813650.9440.1530.3191.315100
2.78-2.8840.23513290.9570.1280.2691.411100
2.88-340.19813660.9620.1090.2271.541100
3-3.1440.1713580.9740.0930.1951.842100
3.14-3.340.1513610.9790.0830.1722.024100
3.3-3.5140.1213600.9840.0660.1382.4100
3.51-3.783.90.10213780.9890.0570.1182.83999.9
3.78-4.163.80.08713740.9890.0490.1013.35599.8
4.16-4.763.80.07213840.9950.0410.0833.4299.4
4.76-63.90.07614000.9920.0420.0883.43198.9
6-503.80.05414510.9970.0310.0632.58796.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FC8

7fc8


Resolution: 2.22→46.48 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.849 / SU ML: 0.165 / SU R Cruickshank DPI: 0.2919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1334 5 %RANDOM
Rwork0.1736 ---
obs0.1767 25158 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 212.91 Å2 / Biso mean: 40.445 Å2 / Biso min: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.05 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.22→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 123 185 4321
Biso mean--33.38 45.62 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124205
X-RAY DIFFRACTIONr_angle_refined_deg1.531.625703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3635535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44322.553188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05615696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7221524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023138
Refine LS restraints NCS

Ens-ID: 1 / Number: 8296 / 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: 2.221→2.279 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 80 -
Rwork0.265 1597 -
all-1677 -
obs--86.4 %

+
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