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- PDB-9m7d: Crystal structure of AsDMS D333N mutant -

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Basic information

Entry
Database: PDB / ID: 9m7d
TitleCrystal structure of AsDMS D333N mutant
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 / Unknown ligand / 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: 2.30000025366 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)122,59536
Polymers120,4302
Non-polymers2,16534
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-364 kcal/mol
Surface area43190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.032, 97.032, 405.183
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

#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-V18), 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
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.96 Å3/Da / Density % sol: 68.94 %
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-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.1819365502 Å / Num. obs: 87319 / % possible obs: 99.97 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.7381444834 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.12
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 8539 / CC1/2: 0.627 / % 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
REFMAC5.8.0403refinement
PHENIX1.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.30000025366→47.1819365502 Å / SU ML: 0.285489962239 / Cross valid method: FREE R-VALUE / σ(F): 1.34881404777 / Phase error: 22.7072719809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226276153165 4390 5.02829129728 %
Rwork0.183655443551 82916 -
obs0.185786985739 87306 99.9874022241 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.308264391 Å2
Refinement stepCycle: LAST / Resolution: 2.30000025366→47.1819365502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8400 0 148 357 8905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01345920435128723
X-RAY DIFFRACTIONf_angle_d1.2421786909511828
X-RAY DIFFRACTIONf_chiral_restr0.06472914210031308
X-RAY DIFFRACTIONf_plane_restr0.008137774992151492
X-RAY DIFFRACTIONf_dihedral_angle_d20.39412249525194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.30000025366-2.32610.3212380618781350.2711073635322708X-RAY DIFFRACTION100
2.3261-2.35350.3370570479151380.2607265216032715X-RAY DIFFRACTION100
2.3535-2.38220.3373646145761510.2622076465632692X-RAY DIFFRACTION100
2.3822-2.41240.3088235395471380.2592255579062755X-RAY DIFFRACTION100
2.4124-2.44410.3141921135961330.2441137774612714X-RAY DIFFRACTION100
2.4441-2.47760.2815136674591360.2238289121532707X-RAY DIFFRACTION100
2.4776-2.5130.309710601771330.2334169591432734X-RAY DIFFRACTION100
2.513-2.55050.2695181662381530.2289129256352749X-RAY DIFFRACTION100
2.5505-2.59030.3168011453641560.232042864922686X-RAY DIFFRACTION100
2.5903-2.63280.2679970949991350.2242698279942734X-RAY DIFFRACTION100
2.6328-2.67820.2846503316671390.2238313055392723X-RAY DIFFRACTION100
2.6782-2.72690.291128253491500.2091000829772712X-RAY DIFFRACTION100
2.7269-2.77930.2502209229161480.2051811259992771X-RAY DIFFRACTION100
2.7793-2.8360.2653036946661410.2079380373672707X-RAY DIFFRACTION100
2.836-2.89770.2229017807041440.1946372866392734X-RAY DIFFRACTION99.9652657173
2.8977-2.96510.2609874096671700.2001717124172718X-RAY DIFFRACTION100
2.9651-3.03920.2572302013261540.1944947861422765X-RAY DIFFRACTION100
3.0392-3.12140.2216402930941600.1965678040812728X-RAY DIFFRACTION100
3.1214-3.21320.2367269579881240.1979113199482749X-RAY DIFFRACTION100
3.2132-3.31690.2122753490641430.1923740934862756X-RAY DIFFRACTION100
3.3169-3.43540.2433357419611520.185629026972782X-RAY DIFFRACTION100
3.4354-3.57290.2381878027381600.1832463352852741X-RAY DIFFRACTION100
3.5729-3.73550.23186093761590.1740705209042780X-RAY DIFFRACTION99.9659863946
3.7355-3.93230.1938301311761480.1663773975572780X-RAY DIFFRACTION100
3.9323-4.17860.2052592778761480.1537934833882779X-RAY DIFFRACTION100
4.1786-4.5010.1609034811331360.139335216952816X-RAY DIFFRACTION100
4.501-4.95350.1796813764891510.1432306234492825X-RAY DIFFRACTION100
4.9535-5.66920.1785445251861380.1599189734642864X-RAY DIFFRACTION100
5.6692-7.13870.2477397756451570.203856963032902X-RAY DIFFRACTION100
7.1387-47.18193655020.1948905486711600.1710819691263090X-RAY DIFFRACTION99.7238416692

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