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- PDB-9ul8: Cryogenic temperature crystal structure of Nmar_1308 protein at 2... -

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Basic information

Entry
Database: PDB / ID: 9ul8
TitleCryogenic temperature crystal structure of Nmar_1308 protein at 2.46 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: 2.46 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 2.46 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
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-65 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.970, 75.970, 209.420
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
11B-311-

HOH

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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.: 35 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
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, 40% v/v PEG 500* MME, 20% w/v PEG 2000

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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: 2.46→37.99 Å / Num. obs: 25601 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.99 / Net I/σ(I): 10.17
Reflection shellResolution: 2.46→2.61 Å / Num. unique obs: 25543 / CC1/2: 0.5

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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: 2.46→37.99 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 50.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4068 2007 7.86 %
Rwork0.3784 --
obs0.3806 25543 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 0 35 5508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055557
X-RAY DIFFRACTIONf_angle_d0.9047509
X-RAY DIFFRACTIONf_dihedral_angle_d6.281766
X-RAY DIFFRACTIONf_chiral_restr0.049894
X-RAY DIFFRACTIONf_plane_restr0.008971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.520.4021460.41660X-RAY DIFFRACTION100
2.52-2.590.43591380.39561646X-RAY DIFFRACTION100
2.59-2.670.42621410.39421661X-RAY DIFFRACTION100
2.67-2.750.36841440.38731681X-RAY DIFFRACTION100
2.75-2.850.4151410.39461659X-RAY DIFFRACTION100
2.85-2.960.42811400.41081666X-RAY DIFFRACTION100
2.96-3.10.45851440.40731659X-RAY DIFFRACTION100
3.1-3.260.36651440.38711679X-RAY DIFFRACTION100
3.26-3.470.39441400.37861694X-RAY DIFFRACTION100
3.47-3.730.41891410.36451670X-RAY DIFFRACTION100
3.73-4.110.42641460.34521688X-RAY DIFFRACTION100
4.11-4.70.37621430.34831695X-RAY DIFFRACTION100
4.7-5.920.4051450.37931711X-RAY DIFFRACTION100
5.92-37.990.41231540.39731767X-RAY DIFFRACTION100

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