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- PDB-9ulb: Cryogenic temperature crystal structure of Nmar_1308 protein at 3... -

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Basic information

Entry
Database: PDB / ID: 9ulb
TitleCryogenic temperature crystal structure of Nmar_1308 protein at 3.29 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsDestan, E. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government119C132 Turkey
CitationJournal: To Be Published
Title: Cryogenic temperature crystal structure of Nmar_1308 protein at 3.29 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

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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
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-65 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.300, 76.300, 210.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 0.3M Sodium fluoride; 0.3M Sodium bromide, 0.3M Sodium iodide, 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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.29→41.12 Å / Num. obs: 10985 / % possible obs: 99.9 % / Redundancy: 13.19 % / CC1/2: 0.98 / Net I/σ(I): 6.06
Reflection shellResolution: 3.29→3.49 Å / Num. unique obs: 1754 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→41.12 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 45.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4147 1097 10.02 %
Rwork0.3561 --
obs0.3621 10945 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.29→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 0 7 5267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045314
X-RAY DIFFRACTIONf_angle_d0.757166
X-RAY DIFFRACTIONf_dihedral_angle_d6.194725
X-RAY DIFFRACTIONf_chiral_restr0.047856
X-RAY DIFFRACTIONf_plane_restr0.008921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.440.40771350.33731210X-RAY DIFFRACTION100
3.44-3.620.36811350.32961225X-RAY DIFFRACTION100
3.62-3.850.37121360.3911202X-RAY DIFFRACTION100
3.85-4.140.42661370.32461219X-RAY DIFFRACTION100
4.14-4.560.38961350.35241233X-RAY DIFFRACTION100
4.56-5.220.44921350.35211220X-RAY DIFFRACTION100
5.22-6.570.44351350.39651249X-RAY DIFFRACTION100
6.57-41.120.41871490.35361290X-RAY DIFFRACTION100

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