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- PDB-9s1p: Crystal structure of the DABA transaminase EctB from the halophil... -

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Basic information

Entry
Database: PDB / ID: 9s1p
TitleCrystal structure of the DABA transaminase EctB from the halophilic and cold-adapted Marinobacter sp. CK1 -Mutant K264A
ComponentsDiaminobutyrate-2-oxoglutarate transaminase
KeywordsTRANSFERASE / pyridoxal phosphate Crystal structure DABA aminotransferase mutant
Function / homologyPYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesMarinobacter sp. CK-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsErlandsen, H. / Leiros, I. / Skogvold, A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Febs J. / Year: 2026
Title: Biochemical characterization and mutational analysis of the tetrameric DABA transaminase EctB from the Arctic bacterium Marinobacter sp. CK1.
Authors: Skogvold, A.C.A. / Leiros, I. / Engh, R.A. / Erlandsen, H.
History
DepositionJul 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Diaminobutyrate-2-oxoglutarate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0755
Polymers46,6471
Non-polymers4284
Water7,242402
1
H: Diaminobutyrate-2-oxoglutarate transaminase
hetero molecules

H: Diaminobutyrate-2-oxoglutarate transaminase
hetero molecules

H: Diaminobutyrate-2-oxoglutarate transaminase
hetero molecules

H: Diaminobutyrate-2-oxoglutarate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,30020
Polymers186,5874
Non-polymers1,71316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area27580 Å2
ΔGint-196 kcal/mol
Surface area48840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.027, 79.893, 180.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11H-504-

NA

21H-728-

HOH

31H-929-

HOH

41H-980-

HOH

51H-999-

HOH

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Components

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Protein , 1 types, 1 molecules H

#1: Protein Diaminobutyrate-2-oxoglutarate transaminase


Mass: 46646.824 Da / Num. of mol.: 1 / Mutation: K264A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter sp. CK-1 (bacteria) / Gene: ectb / Production host: Escherichia coli (E. coli) / References: diaminobutyrate-2-oxoglutarate transaminase

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Non-polymers , 5 types, 406 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M bisTRIS propane pH 7.5 0.1M disodium malonate 25% PEG3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2023
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→48.05 Å / Num. obs: 70422 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 1 / Rmerge(I) obs: 0.018 / Net I/σ(I): 21.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3457 / CC1/2: 0.888 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→48.05 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.075 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16335 3565 5.1 %RANDOM
Rwork0.13807 ---
obs0.13931 66855 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.263 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å2-0 Å2
2---0.33 Å20 Å2
3----1.17 Å2
Refinement stepCycle: 1 / Resolution: 1.55→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 26 402 3621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123442
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163264
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.8254667
X-RAY DIFFRACTIONr_angle_other_deg0.6861.7597533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.581517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62310605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6191.7551761
X-RAY DIFFRACTIONr_mcbond_other1.6031.7551761
X-RAY DIFFRACTIONr_mcangle_it2.2883.152228
X-RAY DIFFRACTIONr_mcangle_other2.2893.1532229
X-RAY DIFFRACTIONr_scbond_it3.3482.11681
X-RAY DIFFRACTIONr_scbond_other3.2742.0851678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.893.6642431
X-RAY DIFFRACTIONr_long_range_B_refined6.10921.284067
X-RAY DIFFRACTIONr_long_range_B_other5.79119.193931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 273 -
Rwork0.196 4861 -
obs--99.94 %

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