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

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Basic information

Entry
Database: PDB / ID: 9ula
TitleCryogenic temperature crystal structure of Nmar_1308 protein at 2.96 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: 2.96 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 2.96 angstrom resolution
Authors: Destan, E. / DeMirci, H.
History
DepositionApr 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 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
D: Enoyl-CoA hydratase/isomerase
E: Enoyl-CoA hydratase/isomerase
F: Enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)158,4986
Polymers158,4986
Non-polymers00
Water84747
1
A: Enoyl-CoA hydratase/isomerase
D: Enoyl-CoA hydratase/isomerase
F: Enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)79,2493
Polymers79,2493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-64 kcal/mol
Surface area26280 Å2
MethodPISA
2
B: Enoyl-CoA hydratase/isomerase
C: Enoyl-CoA hydratase/isomerase
E: Enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)79,2493
Polymers79,2493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-63 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)356.960, 130.530, 82.640
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Enoyl-CoA hydratase/isomerase


Mass: 26416.363 Da / Num. of mol.: 6
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.: 47 / 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: 6.11 Å3/Da / Density % sol: 79.87 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 0.1M Sodium chloride, 0.002M Spermine tetrahydrochloride, 0.05M Bis-Tris pH 7.0, 37% w/v PEG 1000

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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: 2.96→43.92 Å / Num. obs: 77784 / % possible obs: 99.9 % / Redundancy: 11.83 % / CC1/2: 0.98 / Net I/σ(I): 8.85
Reflection shellResolution: 2.96→3.03 Å / Num. unique obs: 12533 / CC1/2: 0.58

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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: 2.96→43.92 Å / SU ML: 0.75 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 55.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4608 2002 2.58 %
Rwork0.442 --
obs0.4425 77691 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.96→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10818 0 0 47 10865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410973
X-RAY DIFFRACTIONf_angle_d0.69514813
X-RAY DIFFRACTIONf_dihedral_angle_d5.4681506
X-RAY DIFFRACTIONf_chiral_restr0.0451765
X-RAY DIFFRACTIONf_plane_restr0.0061911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.030.41961460.40415374X-RAY DIFFRACTION100
3.03-3.120.47911450.4075371X-RAY DIFFRACTION100
3.12-3.210.43661280.41535382X-RAY DIFFRACTION100
3.21-3.310.44121510.41715397X-RAY DIFFRACTION100
3.31-3.430.43691400.42185415X-RAY DIFFRACTION100
3.43-3.570.4521350.43715359X-RAY DIFFRACTION100
3.57-3.730.46531480.43735406X-RAY DIFFRACTION100
3.73-3.930.46781420.44225370X-RAY DIFFRACTION100
3.93-4.170.47271480.44075406X-RAY DIFFRACTION100
4.17-4.490.42481390.44065406X-RAY DIFFRACTION100
4.49-4.940.49561440.44235403X-RAY DIFFRACTION100
4.94-5.660.43971460.4535431X-RAY DIFFRACTION100
5.66-7.120.45911380.46845456X-RAY DIFFRACTION100
7.12-43.920.49041520.46535513X-RAY DIFFRACTION99

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