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- PDB-5ero: Crystal structure of elongation domain of Phomopsis amygdali fusi... -

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Basic information

Entry
Database: PDB / ID: 5ero
TitleCrystal structure of elongation domain of Phomopsis amygdali fusicoccadiene synthase complexed with cobalt ions and pamidronate
ComponentsFusicoccadiene synthase
KeywordsTRANSFERASE / diterpene synthase / lyase
Function / homology
Function and homology information


fusicocca-2,10(14)-diene synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / geranylgeranyl diphosphate synthase activity / isoprenoid biosynthetic process / lyase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / 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: 2.55 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 1.4Sep 27, 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 / 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.ptnr2_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,27018
Polymers118,8583
Non-polymers1,41215
Water2,396133
1
A: Fusicoccadiene synthase
B: Fusicoccadiene synthase
C: Fusicoccadiene synthase
hetero molecules

A: Fusicoccadiene synthase
B: Fusicoccadiene synthase
C: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,54036
Polymers237,7156
Non-polymers2,82530
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area25160 Å2
ΔGint-405 kcal/mol
Surface area69820 Å2
MethodPISA
2
A: Fusicoccadiene synthase
C: Fusicoccadiene synthase
hetero molecules

B: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,27018
Polymers118,8583
Non-polymers1,41215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5740 Å2
ΔGint-142 kcal/mol
Surface area41750 Å2
MethodPISA
3
A: Fusicoccadiene synthase
B: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,18012
Polymers79,2382
Non-polymers94210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-116 kcal/mol
Surface area26450 Å2
MethodPISA
4
C: Fusicoccadiene synthase
hetero molecules

C: Fusicoccadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,18012
Polymers79,2382
Non-polymers94210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5780 Å2
ΔGint-117 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.577, 216.122, 129.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-946-

HOH

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Components

#1: Protein Fusicoccadiene synthase / FS / PaDC4:GGS / Geranylgeranyl diphosphate synthase / GGDP synthase / GGS


Mass: 39619.207 Da / Num. of mol.: 3
Fragment: Geranylgeranyl diphosphate synthase, residues 382-719
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, geranylgeranyl diphosphate synthase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID


Mass: 235.069 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H11NO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.01 M cobalt chloride, 0.1 M sodium acetate (pH 4.6), 1.0 M 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 47383 / % possible obs: 99.5 % / Redundancy: 11.3 % / Net I/σ(I): 21

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q80

2q80


Resolution: 2.55→49.849 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2557 2389 5.05 %
Rwork0.2138 --
obs0.2158 47336 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→49.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7211 0 51 133 7395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037375
X-RAY DIFFRACTIONf_angle_d0.7659957
X-RAY DIFFRACTIONf_dihedral_angle_d14.6492776
X-RAY DIFFRACTIONf_chiral_restr0.0261118
X-RAY DIFFRACTIONf_plane_restr0.0051270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5477-2.59970.32761250.27922344X-RAY DIFFRACTION89
2.5997-2.65620.33521440.27382560X-RAY DIFFRACTION99
2.6562-2.7180.30261450.25842645X-RAY DIFFRACTION100
2.718-2.78590.31310.25732646X-RAY DIFFRACTION100
2.7859-2.86130.3011360.25332637X-RAY DIFFRACTION100
2.8613-2.94540.28921310.26312621X-RAY DIFFRACTION100
2.9454-3.04050.33051440.25262635X-RAY DIFFRACTION100
3.0405-3.14910.29541410.2532678X-RAY DIFFRACTION100
3.1491-3.27520.28191380.24332629X-RAY DIFFRACTION100
3.2752-3.42420.27111340.23172661X-RAY DIFFRACTION100
3.4242-3.60470.25431690.222640X-RAY DIFFRACTION100
3.6047-3.83050.25941380.20492665X-RAY DIFFRACTION100
3.8305-4.12610.2671500.20562666X-RAY DIFFRACTION100
4.1261-4.54110.25111420.18972667X-RAY DIFFRACTION100
4.5411-5.19760.20851470.18272701X-RAY DIFFRACTION100
5.1976-6.54610.28411420.23412719X-RAY DIFFRACTION100
6.5461-49.85870.16881320.16862833X-RAY DIFFRACTION100

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