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- PDB-1hm7: N219L PENTALENENE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1hm7
TitleN219L PENTALENENE SYNTHASE
ComponentsPENTALENENE SYNTHASE
KeywordsLYASE / sesquiterpene synthase / pentalenene / terpene / antibiotic biosynthesis
Function / homology
Function and homology information


pentalenene synthase / pentalenene synthase activity / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
: / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pentalenene synthase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsSeemann, M. / Paschall, C.M. / Christianson, D.W. / Cane, D.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Pentalenene synthase. Analysis of active site residues by site-directed mutagenesis.
Authors: Seemann, M. / Zhai, G. / de Kraker, J.W. / Paschall, C.M. / Christianson, D.W. / Cane, D.E.
History
DepositionDec 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PENTALENENE SYNTHASE
B: PENTALENENE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)75,8372
Polymers75,8372
Non-polymers00
Water46826
1
A: PENTALENENE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)37,9181
Polymers37,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PENTALENENE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)37,9181
Polymers37,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.400, 181.400, 56.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Cell settinghexagonal
Space group name H-MP63
DetailsThe biological assembly is a monomer

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Components

#1: Protein PENTALENENE SYNTHASE / E.C.4.6.1.5


Mass: 37918.273 Da / Num. of mol.: 2 / Mutation: N219L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: UC5319 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55012, EC: 4.6.1.5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: (NH4)2SO4, ethanol, MgCl2, Hepes pH 7.0, farnesyl diphosphate, VAPOR DIFFUSION, SITTING DROP at 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12-7 mg/mlprotein1drop
2100 mMHEPES1droppH7.0
31.5 Mammonium sulfate1reservoir
4100 mMTris-HCl1reservoirpH8.2

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 4, 2000 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 23110 / Num. obs: 23110 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.76 % / Biso Wilson estimate: 45.22 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 11.87
Reflection shellResolution: 2.9→3 Å / Redundancy: 1 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2022 / Rsym value: 0.404 / % possible all: 95.8
Reflection
*PLUS
Highest resolution: 2.9 Å / % possible obs: 97 % / Num. measured all: 63768

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1HM4

1hm4


Resolution: 2.9→20 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.308 2195 9.9 %RANDOM
Rwork0.2633 ---
all0.2633 23827 --
obs0.2633 22227 93.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.745 Å2-9.118 Å20 Å2
2---4.745 Å20 Å2
3---9.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.47 Å
Luzzati d res low-20 Å
Luzzati sigma a0.72 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 0 26 4736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.88
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection
Rfree0.4386 197
Rwork0.3961 -
obs-1828
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.88
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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