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- PDB-4mc8: Hedycaryol synthase in complex with HEPES -

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Basic information

Entry
Database: PDB / ID: 4mc8
TitleHedycaryol synthase in complex with HEPES
ComponentsPutative sesquiterpene cyclase
KeywordsLYASE / cyclase / terpenoid / Terpene alpha domain class I / helix break / helix dipol
Function / homology
Function and homology information


(2Z,6E)-hedycaryol synthase / terpene synthase activity / terpenoid 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
(2Z,6E)-hedycaryol synthase
Similarity search - Component
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBaer, P. / Rabe, P. / Cirton, C. / Oliveira Mann, C. / Kaufmann, N. / Groll, M. / Dickschat, J.
CitationJournal: Chembiochem / Year: 2014
Title: Hedycaryol synthase in complex with nerolidol reveals terpene cyclase mechanism.
Authors: Baer, P. / Rabe, P. / Citron, C.A. / de Oliveira Mann, C.C. / Kaufmann, N. / Groll, M. / Dickschat, J.S.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Putative sesquiterpene cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9402
Polymers38,7011
Non-polymers2381
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.770, 80.770, 271.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative sesquiterpene cyclase


Mass: 38701.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (bacteria)
Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054
Gene: KSE_00200t, KSE_76540t / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E4MYY0, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M, HEPES, 20 mM MgCl2, 21% Sodium polyacrylate 5100, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38.71 Å / Num. all: 42526 / Num. obs: 42016 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 5.94 / Mean I/σ(I) obs: 2.1 / % possible all: 93

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MC3

4mc3


Resolution: 1.9→38.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.646 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.14 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21926 2101 5 %RANDOM
Rwork0.18452 ---
obs0.18628 39915 99.18 %-
all-42016 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.959 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å21.86 Å20 Å2
2--1.86 Å20 Å2
3----6.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 15 208 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192411
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9553280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5275292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44223.14121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73315382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9961526
X-RAY DIFFRACTIONr_chiral_restr0.080.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211853
X-RAY DIFFRACTIONr_rigid_bond_restr2.91632411
X-RAY DIFFRACTIONr_sphericity_free48.257572
X-RAY DIFFRACTIONr_sphericity_bonded45.71152496
LS refinement shellResolution: 1.9→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 140 -
Rwork0.334 2670 -
obs--92.22 %
Refinement TLS params.Method: refined / Origin x: -16.6239 Å / Origin y: 34.4506 Å / Origin z: 7.6602 Å
111213212223313233
T0.013 Å20.0026 Å20.0027 Å2-0.0303 Å2-0.002 Å2--0.0218 Å2
L0.1028 °2-0.0102 °20.0066 °2-0.0389 °20.0425 °2--0.0501 °2
S-0.0109 Å °-0.0539 Å °-0.0023 Å °0.0117 Å °0.0078 Å °0.0008 Å °0.0118 Å °-0.0006 Å °0.0031 Å °

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