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- PDB-5zy8: Crystal structure of C terminal truncated HadBC (3R-Hydroxyacyl-A... -

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Basic information

Entry
Database: PDB / ID: 5zy8
TitleCrystal structure of C terminal truncated HadBC (3R-Hydroxyacyl-ACP Dehydratase) complex from Mycobacterium tuberculosis
Components
  • 3-hydroxyacyl-ACP dehydratase
  • UPF0336 protein Rv0637
KeywordsLYASE / Heterodimer / Complex / Hot-dog fold / Dehydratase
Function / homology
Function and homology information


(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / fatty acid elongation / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / plasma membrane
Similarity search - Function
Dehydratase subunit HadA-like / : / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
(3R)-hydroxyacyl-ACP dehydratase subunit HadB / : / UPF0336 protein Rv0637
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.899 Å
AuthorsSingh, B.K. / Biswas, R. / Bhattacharyya, S. / Basak, A. / Das, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
BT/PR12404/BRB/10/1362/2014 India
CitationJournal: Febs J. / Year: 2022
Title: The C-terminal end of mycobacterial HadBC regulates AcpM interaction during the FAS-II pathway: a structural perspective.
Authors: Singh, B.K. / Biswas, R. / Bhattacharyya, S. / Basak, A. / Das, A.K.
History
DepositionMay 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0336 protein Rv0637
B: 3-hydroxyacyl-ACP dehydratase
C: UPF0336 protein Rv0637
D: 3-hydroxyacyl-ACP dehydratase


Theoretical massNumber of molelcules
Total (without water)66,1774
Polymers66,1774
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-39 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.417, 119.417, 99.177
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21(chain D and resid 2 through 142)
12(chain A and ((resid 3 through 4 and (name N...
22(chain C and (resid 3 through 113 or resid 119 through 143))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAALAALAchain BBB2 - 1422 - 142
211ALAALAALAALA(chain D and resid 2 through 142)DD2 - 1422 - 142
112LEULEULYSLYS(chain A and ((resid 3 through 4 and (name N...AA3 - 43 - 4
122LEULEUMETMET(chain A and ((resid 3 through 4 and (name N...AA3 - 1433 - 143
132LEULEUMETMET(chain A and ((resid 3 through 4 and (name N...AA3 - 1433 - 143
142LEULEUMETMET(chain A and ((resid 3 through 4 and (name N...AA3 - 1433 - 143
152LEULEUMETMET(chain A and ((resid 3 through 4 and (name N...AA3 - 1433 - 143
212LEULEUASPASP(chain C and (resid 3 through 113 or resid 119 through 143))CC3 - 1133 - 113
222ASPASPMETMET(chain C and (resid 3 through 113 or resid 119 through 143))CC119 - 143119 - 143

NCS ensembles :
ID
1
2

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Components

#1: Protein UPF0336 protein Rv0637 / HadC subunit


Mass: 18138.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0637, MTCY20H10.18 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFJ9
#2: Protein 3-hydroxyacyl-ACP dehydratase / HadB subunit


Mass: 14949.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: LH57_03445 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L0T618, UniProt: I6WYY7*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 2% v/v 1,4-dioxane, 0.1M Tris HCl, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.899→103.418 Å / Num. obs: 18426 / % possible obs: 99.6 % / Redundancy: 15 % / Biso Wilson estimate: 59.13 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.152 / Rsym value: 0.147 / Net I/av σ(I): 5.1 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.9-3.0615.21.0260.826440.2691.0611.02699.7
3.06-3.2415.30.6441.225210.1680.6660.64499.8
3.24-3.4615.20.4071.923690.1070.4210.40799.9
3.46-3.7415.20.2523.122150.0660.260.252100
3.74-4.115.10.1654.720700.0440.1710.165100
4.1-4.58150.0938.318450.0250.0960.093100
4.58-5.2914.90.06811.216490.0180.070.068100
5.29-6.4814.80.07110.714210.0190.0730.071100
6.48-9.1714.20.03718.411140.010.0390.037100
9.17-19.54412.70.02425.15780.0070.0250.02490.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.551
Highest resolutionLowest resolution
Rotation19.55 Å3.08 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RLJ

4rlj


Resolution: 2.899→19.544 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.69
RfactorNum. reflection% reflection
Rfree0.228 849 4.61 %
Rwork0.1856 --
obs0.1877 18408 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.62 Å2 / Biso mean: 65.6146 Å2 / Biso min: 26.92 Å2
Refinement stepCycle: final / Resolution: 2.899→19.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 0 119 4386
Biso mean---50.88 -
Num. residues----553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084355
X-RAY DIFFRACTIONf_angle_d1.2345910
X-RAY DIFFRACTIONf_chiral_restr0.079673
X-RAY DIFFRACTIONf_plane_restr0.007760
X-RAY DIFFRACTIONf_dihedral_angle_d13.6752561
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1226X-RAY DIFFRACTION10.676TORSIONAL
12D1226X-RAY DIFFRACTION10.676TORSIONAL
21A1190X-RAY DIFFRACTION10.676TORSIONAL
22C1190X-RAY DIFFRACTION10.676TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8988-3.07980.35531310.264828763007
3.0798-3.31650.24641190.227229213040
3.3165-3.64830.24791420.198128783020
3.6483-4.17170.23871530.189129133066
4.1717-5.23910.21751470.159429343081
5.2391-19.54460.19221570.164630373194
Refinement TLS params.Method: refined / Origin x: 35.8975 Å / Origin y: -24.9445 Å / Origin z: 42.5885 Å
111213212223313233
T0.3119 Å20.1535 Å20.1295 Å2-0.2884 Å20.1523 Å2--0.3369 Å2
L0.7082 °20.6553 °2-0.5445 °2-0.9256 °2-0.2952 °2--1.3341 °2
S0.112 Å °0.2541 Å °0.2166 Å °0.3152 Å °0.1754 Å °0.2795 Å °-0.2292 Å °-0.3234 Å °0.4785 Å °
Refinement TLS groupSelection details: all

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