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- PDB-9m7e: Crystal structure of AsDMS D333N mutant in complex with drimenyl ... -

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Basic information

Entry
Database: PDB / ID: 9m7e
TitleCrystal structure of AsDMS D333N mutant in complex with drimenyl phosphate
ComponentsHaloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
KeywordsBIOSYNTHETIC PROTEIN / Terpene cyclase / Haloacid dehalogenase / Phosphatase / Biosynthesis
Function / homologyHaloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily / HAD-like superfamily / : / FARNESYL DIPHOSPHATE / Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
Function and homology information
Biological speciesAquimarina spongiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9000384384 Å
AuthorsFujiyama, K. / Vo, N.N.Q. / Takahashi, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00416 Japan
Japan Society for the Promotion of Science (JSPS)21J01340 Japan
CitationJournal: Chem Sci / Year: 2025
Title: Structural insights into a bacterial terpene cyclase fused with haloacid Dehalogenase-like phosphatase.
Authors: Fujiyama, K. / Takagi, H. / Vo, N.N.Q. / Morita, N. / Nogawa, T. / Takahashi, S.
History
DepositionMar 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
B: Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,14925
Polymers120,4302
Non-polymers2,71923
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-206 kcal/mol
Surface area42150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.437, 97.437, 403.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED


Mass: 60214.902 Da / Num. of mol.: 2 / Mutation: deletion (M1-V189), D333N
Source method: isolated from a genetically manipulated source
Details: Initial 'GSH' is from the amino acid residues in the thrombin recognition site. deletion: M1-V18 engineering mutation: D333N
Source: (gene. exp.) Aquimarina spongiae (bacteria) / Gene: SAMN04488508_102320 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M6CXF0

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Non-polymers , 6 types, 40 molecules

#2: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-A1MAK / drimenyl phosphate / (2,5,5,8~{a}-tetramethyl-1,2,3,4,4~{a},6,7,8-octahydronaphthalen-1-yl)methyl dihydrogen phosphate


Mass: 302.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H27O4P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.97 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 293 K / Method: microfluidic
Details: 1.72 M ammonium sulfate, 0.095 M MES-NaOH pH6.5, 0.005 M MES-NaOH pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.9→48.37 Å / Num. obs: 44369 / % possible obs: 99.93 % / Redundancy: 13.2 % / Biso Wilson estimate: 71.8384387996 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.77
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 4328 / CC1/2: 0.551 / % possible all: 99.98

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Processing

Software
NameVersionClassification
XDSVERSION Jan 10, 2022 BUILT=20220820data reduction
XDSVERSION Jan 10, 2022 BUILT=20220820data scaling
pointless1.12.10data scaling
Aimless0.7.9data scaling
PHASER2.8.3phasing
Coot0.9.8.92model building
REFMAC5.8.0411refinement
PHENIX1.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.9000384384→48.3667021781 Å / SU ML: 0.426548054545 / Cross valid method: FREE R-VALUE / σ(F): 1.35407072819 / Phase error: 27.1047048811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242734687487 2259 5.09288484083 %
Rwork0.201551739575 42097 -
obs0.203722053666 44356 99.9707002637 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.6794003656 Å2
Refinement stepCycle: LAST / Resolution: 2.9000384384→48.3667021781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8353 0 151 17 8521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001856341173988677
X-RAY DIFFRACTIONf_angle_d0.42299146170111768
X-RAY DIFFRACTIONf_chiral_restr0.03787485322061304
X-RAY DIFFRACTIONf_plane_restr0.002645827039161481
X-RAY DIFFRACTIONf_dihedral_angle_d17.58721354045183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9000384384-2.96310.3734279572861450.3485229443342563X-RAY DIFFRACTION100
2.9631-3.0320.3840410100621230.3200277651332586X-RAY DIFFRACTION99.963099631
3.032-3.10780.3810860268951350.3150443596612577X-RAY DIFFRACTION100
3.1078-3.19180.3473506025591420.3100524430692567X-RAY DIFFRACTION99.963099631
3.1918-3.28570.3612710800211320.3090069561632593X-RAY DIFFRACTION99.9633162142
3.2857-3.39180.3301207445221260.2630677199912587X-RAY DIFFRACTION100
3.3918-3.51290.3126114265971510.2504223480382595X-RAY DIFFRACTION100
3.5129-3.65360.2687159153511250.2210639959012607X-RAY DIFFRACTION100
3.6536-3.81980.2360418561351380.2048841297572630X-RAY DIFFRACTION100
3.8198-4.02110.2410464639491500.1942309968462585X-RAY DIFFRACTION100
4.0211-4.27290.2167087119341430.1701675111392646X-RAY DIFFRACTION100
4.2729-4.60250.2008270244951310.1491365459162632X-RAY DIFFRACTION100
4.6025-5.06530.1971497343041400.1550611059312652X-RAY DIFFRACTION100
5.0653-5.79720.2126666159891640.1709518087392660X-RAY DIFFRACTION100
5.7972-7.29980.2297343603911480.1996565576692724X-RAY DIFFRACTION100
7.2998-48.36670217810.1879241628171660.1634077648572893X-RAY DIFFRACTION99.6741609645

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