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- PDB-9s1q: Crystal structure of the DABA transaminase EctB from the halophil... -

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Basic information

Entry
Database: PDB / ID: 9s1q
TitleCrystal structure of the DABA transaminase EctB from the halophilic and cold-adapted Marinobacter sp. CK1
ComponentsDiaminobutyrate-2-oxoglutarate transaminase
KeywordsTRANSFERASE / pyridoxal phosphate Crystal structure DABA aminotransferase
Function / homology4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesMarinobacter sp. CK-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsErlandsen, H. / Skogvold, A. / Leiros, I.
Funding support Norway, 1items
OrganizationGrant numberCountry
Other government Norway
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
A: Diaminobutyrate-2-oxoglutarate transaminase
B: Diaminobutyrate-2-oxoglutarate transaminase
C: Diaminobutyrate-2-oxoglutarate transaminase
D: Diaminobutyrate-2-oxoglutarate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,08911
Polymers186,8204
Non-polymers1,2697
Water11,548641
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.648, 99.332, 112.698
Angle α, β, γ (deg.)90.00, 104.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Diaminobutyrate-2-oxoglutarate transaminase


Mass: 46704.926 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M bisTRIS propane pH 8, 0.2 M disodium malonate, 19.6 % PEG3350 (w/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2→45.53 Å / Num. obs: 115468 / % possible obs: 99.6 % / Redundancy: 1.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1 / Num. unique obs: 5716 / CC1/2: 0.451 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.13 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 10.411 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20815 5736 5 %RANDOM
Rwork0.1654 ---
obs0.16752 109707 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.475 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20.67 Å2
2--0.64 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 2→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12768 0 82 641 13491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01213083
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612379
X-RAY DIFFRACTIONr_angle_refined_deg2.1771.82517635
X-RAY DIFFRACTIONr_angle_other_deg0.741.75928591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67751668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.819556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.462102276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.21939
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022868
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_it2.8972.456684
X-RAY DIFFRACTIONr_mcbond_other2.8972.456684
X-RAY DIFFRACTIONr_mcangle_it3.6214.3918348
X-RAY DIFFRACTIONr_mcangle_other3.624.3918349
X-RAY DIFFRACTIONr_scbond_it4.3722.8626399
X-RAY DIFFRACTIONr_scbond_other4.3722.8626400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.145.0719288
X-RAY DIFFRACTIONr_long_range_B_refined6.98823.4114439
X-RAY DIFFRACTIONr_long_range_B_other6.96623.0914329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 405 -
Rwork0.309 8080 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0297-0.0002-0.19050.84240.41240.64150.00190.1633-0.0939-0.07740.0421-0.08760.04780.0392-0.04390.05510.0382-0.03570.1481-0.06890.077262.5758-27.333518.3757
21.1378-0.4385-0.13210.8740.37530.52670.01780.1892-0.2570.02180.0128-0.00980.1408-0.0488-0.03060.1103-0.0071-0.02420.1997-0.08950.085234.3715-37.570411.1443
30.76220.00410.17481.18270.50840.58820.00260.08290.1075-0.0452-0.06350.1019-0.0168-0.08070.06090.01390.00340.00990.0540.01120.03914.09540.762436.8206
40.9531-0.1334-0.12540.72110.50020.74620.00460.01510.10890.05450.0341-0.07490.01710.0824-0.03870.0294-0.00040.01440.02420.00860.038342.364511.189243.5867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 502
2X-RAY DIFFRACTION2B1 - 501
3X-RAY DIFFRACTION3C1 - 502
4X-RAY DIFFRACTION4D1 - 502

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