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- PDB-1ps1: PENTALENENE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1ps1
TitlePENTALENENE SYNTHASE
ComponentsPENTALENENE SYNTHASE
KeywordsANTIBIOTIC BIOSYNTHESIS / SESQUITERPENE CYCLASE / LYASE
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
TRIMETHYL LEAD ION / Pentalenene synthase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsLesburg, C.A. / Christianson, D.W.
Citation
Journal: Science / Year: 1997
Title: Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology.
Authors: Lesburg, C.A. / Zhai, G. / Cane, D.E. / Christianson, D.W.
#1: Journal: Protein Sci. / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Recombinant Pentalenene Synthase
Authors: Lesburg, C.A. / Lloyd, M.D. / Cane, D.E. / Christianson, D.W.
#2: Journal: Biochemistry / Year: 1994
Title: Pentalenene Synthase. Purification, Molecular Cloning, Sequencing, and High-Level Expression in Escherichia Coli of a Terpenoid Cyclase from Streptomyces Uc5319
Authors: Cane, D.E. / Sohng, J.K. / Lamberson, C.R. / Rudnicki, S.M. / Wu, Z. / Lloyd, M.D. / Oliver, J.S. / Hubbard, B.R.
History
DepositionMar 23, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENTALENENE SYNTHASE
B: PENTALENENE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3533
Polymers76,1012
Non-polymers2521
Water1,18966
1
A: PENTALENENE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3032
Polymers38,0501
Non-polymers2521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PENTALENENE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)38,0501
Polymers38,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.720, 178.720, 56.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.298373, -0.228446, -0.926707), (-0.275203, -0.909105, 0.312715), (-0.913913, 0.348338, 0.208384)
Vector: 126.707, 96.221, 70.512)

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Components

#1: Protein PENTALENENE SYNTHASE


Mass: 38050.414 Da / Num. of mol.: 2
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: Chemical ChemComp-PBM / TRIMETHYL LEAD ION


Mass: 252.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9Pb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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 growpH: 7
Details: CRYSTALLIZED FROM 1.5M AMMONIUM SULFATE, 100 MM HEPES, PH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Lesburg, C.A., (1995) Protein Sci., 4, 2436.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.4-1.8 Mammonium sulfate1reservoir
31.0-1.4 Msodium citrate1reservoir
40.8-1.8 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914
DetectorType: PRINCETON 2K / Detector: CCD / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. obs: 28128 / % possible obs: 87.5 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.056 / Net I/σ(I): 13.8
Reflection shellResolution: 2.6→2.69 Å / Rsym value: 0.158 / % possible all: 57.7
Reflection
*PLUS
Num. measured all: 70683 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Rmerge(I) obs: 0.158

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLOMONphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.6→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1342 5 %RANDOM
Rwork0.198 ---
obs0.198 26500 82.6 %-
Displacement parametersBiso mean: 52.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 1 66 4917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.78
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.62
X-RAY DIFFRACTIONx_mcangle_it24
X-RAY DIFFRACTIONx_scbond_it2.62
X-RAY DIFFRACTIONx_scangle_it24
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 17.4 Å2 / Rms dev position: 0.43 Å / Weight Biso : 44.4 / Weight position: 9
LS refinement shellResolution: 2.6→2.66 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.431 56 5 %
Rwork0.316 917 -
obs--46.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.71

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