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- PDB-9ul9: Cryogenic temperature crystal structure of Nmar_1308 protein at 2... -

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Basic information

Entry
Database: PDB / ID: 9ul9
TitleCryogenic temperature crystal structure of Nmar_1308 protein at 2.71 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: 2.71 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 2.71 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
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-64 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.190, 74.190, 206.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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 0.1197 (bacteria) / References: UniProt: A9A2G5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate, 1.0 M 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: 2.71→40.29 Å / Num. obs: 34665 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.96 / Net I/σ(I): 8.19
Reflection shellResolution: 2.71→2.87 Å / Num. unique obs: 5506 / CC1/2: 0.62

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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: 2.71→40.29 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 47.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.396 2013 5.82 %
Rwork0.3704 --
obs0.3719 34613 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 0 62 5535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025545
X-RAY DIFFRACTIONf_angle_d0.4767491
X-RAY DIFFRACTIONf_dihedral_angle_d4.971764
X-RAY DIFFRACTIONf_chiral_restr0.039893
X-RAY DIFFRACTIONf_plane_restr0.004968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.780.40571480.35582327X-RAY DIFFRACTION100
2.78-2.850.37851500.37432395X-RAY DIFFRACTION100
2.85-2.940.37161380.36362277X-RAY DIFFRACTION100
2.94-3.030.40421360.37352313X-RAY DIFFRACTION100
3.03-3.140.40831600.38112333X-RAY DIFFRACTION100
3.14-3.270.40751520.37112325X-RAY DIFFRACTION100
3.27-3.410.45841440.36862315X-RAY DIFFRACTION100
3.41-3.590.40451340.37752330X-RAY DIFFRACTION100
3.59-3.820.39471520.35252317X-RAY DIFFRACTION100
3.82-4.110.39521480.35272361X-RAY DIFFRACTION100
4.11-4.530.36021400.35652303X-RAY DIFFRACTION100
4.53-5.180.39091480.36722327X-RAY DIFFRACTION100
5.18-6.520.46511360.39972338X-RAY DIFFRACTION100
6.52-40.290.34831270.39022339X-RAY DIFFRACTION100

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