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- PDB-4mc0: Hedycaryol apo -

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Basic information

Entry
Database: PDB / ID: 4mc0
TitleHedycaryol apo
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: 2.7 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 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sesquiterpene cyclase
B: Putative sesquiterpene cyclase


Theoretical massNumber of molelcules
Total (without water)77,4032
Polymers77,4032
Non-polymers00
Water1,982110
1
A: Putative sesquiterpene cyclase


Theoretical massNumber of molelcules
Total (without water)38,7011
Polymers38,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative sesquiterpene cyclase


Theoretical massNumber of molelcules
Total (without water)38,7011
Polymers38,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.380, 80.600, 97.550
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative sesquiterpene cyclase


Mass: 38701.473 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TRIS, 1.6 M (NH4)2SO4, pH 8.0, 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: May 5, 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: 2.7→30 Å / Num. all: 25308 / Num. obs: 24119 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.5 / % possible all: 97.3

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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: HcS Nerolidol complex

Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 26.638 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24736 1206 5 %RANDOM
Rwork0.20665 ---
obs0.20865 22913 95.31 %-
all-24119 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.583 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å20 Å2-0.08 Å2
2---5 Å2-0 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 0 110 4721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194724
X-RAY DIFFRACTIONr_angle_refined_deg0.9721.9516428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1425572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39122.821234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87115752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.421552
X-RAY DIFFRACTIONr_chiral_restr0.0710.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213642
X-RAY DIFFRACTIONr_rigid_bond_restr2.83534722
X-RAY DIFFRACTIONr_sphericity_free41.989545
X-RAY DIFFRACTIONr_sphericity_bonded11.58254687
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 88 -
Rwork0.321 1681 -
obs--97.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2936-0.0557-0.17520.4639-0.00690.10830.00490.0019-0.0123-0.0207-0.0050.0151-0.0023-0.00260.00020.02090.0038-0.0290.02130.00470.0455134.5786-17.7259101.873
20.2738-0.0357-0.16430.302-0.05510.20170.01130.0209-0.01960.0172-0.0034-0.014-0.0184-0.0172-0.0080.0141-0.0048-0.02320.01190.00850.0548141.4221-42.8747141.1448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 312
2X-RAY DIFFRACTION2B4 - 312

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