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- PDB-9m7f: Crystal structure of AsDMS D333N mutant in complex with farnesyl ... -

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Basic information

Entry
Database: PDB / ID: 9m7f
TitleCrystal structure of AsDMS D333N mutant in complex with farnesyl pyrophosphate
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: 2.60002725624 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)123,57927
Polymers120,4302
Non-polymers3,14925
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-206 kcal/mol
Surface area42510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.546, 96.546, 401.409
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, 219 molecules

#2: Chemical
ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H28O7P2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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: 1.04 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.6→49.3031591263 Å / Num. obs: 59769 / % possible obs: 99.95 % / Redundancy: 13.5 % / Biso Wilson estimate: 53.557292161 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.84
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.85 / Num. unique obs: 5855 / CC1/2: 0.72 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSVERSION Jan 10, 2022 BUILT=20220120data reduction
XDSVERSION Jan 10, 2022 BUILT=20220120data scaling
pointless1.12.10data scaling
Aimless0.7.9data scaling
PHASER2.8.3phasing
Coot0.9.8.92model building
REFMAC5.8.0352refinement
PHENIX1.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.60002725624→49.3031591263 Å / SU ML: 0.364383915952 / Cross valid method: FREE R-VALUE / σ(F): 1.3523052928 / Phase error: 24.4783007541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235672843876 3043 5.09203480589 %
Rwork0.192910874098 56717 -
obs0.195099463997 59760 99.9799237101 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.7535927991 Å2
Refinement stepCycle: LAST / Resolution: 2.60002725624→49.3031591263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8397 0 179 194 8770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008248987531298746
X-RAY DIFFRACTIONf_angle_d0.94684315546511847
X-RAY DIFFRACTIONf_chiral_restr0.05039714620011307
X-RAY DIFFRACTIONf_plane_restr0.005877045642221494
X-RAY DIFFRACTIONf_dihedral_angle_d20.83661024785218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.60002725624-2.64070.4231776854481510.3135546161592497X-RAY DIFFRACTION100
2.6407-2.68390.3011721840751430.2908053101882550X-RAY DIFFRACTION100
2.6839-2.73020.3154672366261320.2640626192812526X-RAY DIFFRACTION100
2.7302-2.77990.3368189807481370.2492579645722516X-RAY DIFFRACTION100
2.7799-2.83330.2961383603991290.2501072032052535X-RAY DIFFRACTION100
2.8333-2.89120.3155390034781350.2424516727252519X-RAY DIFFRACTION100
2.8912-2.9540.3043162038861270.2478668359462546X-RAY DIFFRACTION100
2.954-3.02270.2913643224171580.2497713382492545X-RAY DIFFRACTION100
3.0227-3.09830.3064988937551350.2511665379542524X-RAY DIFFRACTION100
3.0983-3.18210.3223704845641330.2488007846092552X-RAY DIFFRACTION100
3.1821-3.27570.2954652554241270.2276401820762554X-RAY DIFFRACTION100
3.2757-3.38140.2459480726941480.2158923788052528X-RAY DIFFRACTION100
3.3814-3.50220.2316872334061400.2008187032662568X-RAY DIFFRACTION100
3.5022-3.64240.2428845309981270.1924258661572563X-RAY DIFFRACTION100
3.6424-3.80810.2263859848431500.1753503655262572X-RAY DIFFRACTION100
3.8081-4.00880.2010378235461580.1611232198382581X-RAY DIFFRACTION99.9270339292
4.0088-4.25980.1934253998171150.1559855016452588X-RAY DIFFRACTION100
4.2598-4.58850.1820855631521310.1391099905882634X-RAY DIFFRACTION100
4.5885-5.04980.2075459587961210.1546165023932628X-RAY DIFFRACTION100
5.0498-5.77960.2160341447711400.1758240250942641X-RAY DIFFRACTION100
5.7796-7.27790.2240553191051450.2043593653982690X-RAY DIFFRACTION100
7.2779-49.30315912630.1902382586561610.1746052623072860X-RAY DIFFRACTION99.6700758825

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