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- PDB-9ulc: Ambient temperature crystal structure of Nmar_1308 protein at 3.3... -

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Basic information

Entry
Database: PDB / ID: 9ulc
TitleAmbient temperature crystal structure of Nmar_1308 protein at 3.33 angstrom resolution
ComponentsEnoyl-CoA hydratase/isomerase
KeywordsSTRUCTURAL PROTEIN / bifunctional enzyme / carbon fixation
Function / homologyEnoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / fatty acid beta-oxidation / ClpP/crotonase-like domain superfamily / lyase activity / Enoyl-CoA hydratase/isomerase
Function and homology information
Biological speciesNitrosopumilus maritimus SCM1 (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsDestan, E. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government119C132 Turkey
CitationJournal: To Be Published
Title: Ambient temperature crystal structure of Nmar_1308 protein at 3.33 angstrom resolution
Authors: Destan, E. / DeMirci, H.
History
DepositionApr 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase/isomerase
B: Enoyl-CoA hydratase/isomerase
C: Enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)79,2493
Polymers79,2493
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-64 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.130, 81.130, 216.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-219-

ASP

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Components

#1: Protein Enoyl-CoA hydratase/isomerase


Mass: 26416.363 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosopumilus maritimus SCM1 (archaea)
Gene: Nmar_1308 / Production host: Escherichia coli (E. coli) / References: UniProt: A9A2G5
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 1.0M Tris (base), BICINE pH 8.5, 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 3.33→32.46 Å / Num. obs: 55194 / % possible obs: 100 % / Redundancy: 69.84 % / CC1/2: 0.91 / CC star: 0.97 / Net I/σ(I): 4.23
Reflection shellResolution: 3.33→3.47 Å / Mean I/σ(I) obs: 1.95 / Num. unique obs: 2748 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.33→24.04 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3726 187 1.54 %
Rwork0.323 --
obs0.3238 12174 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.33→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 0 0 5473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035535
X-RAY DIFFRACTIONf_angle_d0.6797477
X-RAY DIFFRACTIONf_dihedral_angle_d6.581762
X-RAY DIFFRACTIONf_chiral_restr0.07892
X-RAY DIFFRACTIONf_plane_restr0.005965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.33-3.540.3256280.31781945X-RAY DIFFRACTION98
3.54-3.810.3893310.33541964X-RAY DIFFRACTION99
3.81-4.190.4168300.30811983X-RAY DIFFRACTION100
4.19-4.790.3808330.3092012X-RAY DIFFRACTION100
4.8-6.020.3551320.31811997X-RAY DIFFRACTION100
6.03-24.040.3575330.34392086X-RAY DIFFRACTION100

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