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- PDB-5erm: Crystal structure of cyclization domain of Phomopsis amygdali fus... -

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Basic information

Entry
Database: PDB / ID: 5erm
TitleCrystal structure of cyclization domain of Phomopsis amygdali fusicoccadiene synthase complexed with magnesium ions and pamidronate
ComponentsFusicoccadiene synthase
KeywordsLYASE / diterpene cyclase / terpenoids
Function / homology
Function and homology information


fusicocca-2,10(14)-diene synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / ketone biosynthetic process / farnesyltranstransferase activity / isoprenoid biosynthetic process / lyase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PAMIDRONATE / Fusicoccadiene synthase
Similarity search - Component
Biological speciesPhomopsis amygdali (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsChen, M. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase.
Authors: Chen, M. / Chou, W.K. / Toyomasu, T. / Cane, D.E. / Christianson, D.W.
History
DepositionNov 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusicoccadiene synthase
B: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,07312
Polymers83,3872
Non-polymers68710
Water3,315184
1
A: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0376
Polymers41,6931
Non-polymers3435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0376
Polymers41,6931
Non-polymers3435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.295, 143.295, 118.261
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Fusicoccadiene synthase / FS / PaDC4:GGS / Fusicocca-2 / 10(14)-diene synthase / Diterpene cyclase 4 / DC 4


Mass: 41693.266 Da / Num. of mol.: 2 / Fragment: Fusicocca-2,10(14)-diene synthase, residues 1-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phomopsis amygdali (fungus) / Gene: PaFS / Production host: Escherichia coli (E. coli)
References: UniProt: A2PZA5, fusicocca-2,10(14)-diene synthase
#2: Chemical ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID


Mass: 235.069 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H11NO7P2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 1.75 M sodium formate, 0.25 M magnesium formate, 0.1 M sodium acetate (pH4.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 62273 / % possible obs: 99.9 % / Redundancy: 19.1 % / Net I/σ(I): 37.2

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.303→46.904 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2062 3178 5.11 %
Rwork0.1778 --
obs0.1818 62237 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→46.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4991 0 34 184 5209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045148
X-RAY DIFFRACTIONf_angle_d0.9316982
X-RAY DIFFRACTIONf_dihedral_angle_d14.9211888
X-RAY DIFFRACTIONf_chiral_restr0.048752
X-RAY DIFFRACTIONf_plane_restr0.003886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3033-2.3430.29461590.28632877X-RAY DIFFRACTION94
2.343-2.38560.26071870.27932933X-RAY DIFFRACTION94
2.3856-2.43140.30851680.2612880X-RAY DIFFRACTION94
2.4314-2.4810.29491290.26282972X-RAY DIFFRACTION96
2.481-2.5350.2951410.2652913X-RAY DIFFRACTION95
2.535-2.59390.28181530.25242940X-RAY DIFFRACTION95
2.5939-2.65870.29211690.25412927X-RAY DIFFRACTION95
2.6587-2.73050.28161420.24392930X-RAY DIFFRACTION95
2.7305-2.81080.26571750.23122945X-RAY DIFFRACTION94
2.8108-2.90150.29121700.22392914X-RAY DIFFRACTION94
2.9015-3.00510.25871670.22132907X-RAY DIFFRACTION95
3.0051-3.12520.22611770.21822934X-RAY DIFFRACTION94
3.1252-3.26730.22931340.21112966X-RAY DIFFRACTION96
3.2673-3.43930.21151460.19282959X-RAY DIFFRACTION95
3.4393-3.65430.20761660.18062943X-RAY DIFFRACTION95
3.6543-3.93580.17421610.16142949X-RAY DIFFRACTION95
3.9358-4.33070.20381460.13893001X-RAY DIFFRACTION95
4.3307-4.95450.14221650.13732976X-RAY DIFFRACTION95
4.9545-6.23150.18871550.15383026X-RAY DIFFRACTION95
6.2315-28.53950.17591670.14333104X-RAY DIFFRACTION95

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