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- PDB-6sxl: Crystal structure of CrtE -

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Basic information

Entry
Database: PDB / ID: 6sxl
TitleCrystal structure of CrtE
Components(Geranylgeranyl pyrophosphate synthase) x 2
KeywordsTRANSFERASE / Isoprenoid / prenyltransferase
Function / homology
Function and homology information


geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / prenyltransferase activity / metal ion binding / cytoplasm
Similarity search - Function
: / 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
PHOSPHATE ION / Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFeng, Y. / Morgan, R.M.L. / Nixon, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Union (EU)PHOTOFUEL - No 640720 United Kingdom
CitationJournal: Front Plant Sci / Year: 2020
Title: Crystal Structure of Geranylgeranyl Pyrophosphate Synthase (CrtE) Involved in Cyanobacterial Terpenoid Biosynthesis.
Authors: Feng, Y. / Morgan, R.M.L. / Fraser, P.D. / Hellgardt, K. / Nixon, P.J.
History
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8634
Polymers57,6732
Non-polymers1902
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-50 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.203, 89.470, 107.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 11 - 300

Dom-IDComponent-IDAuth asym-IDLabel asym-IDLabel seq-ID
11BB1 - 258
22AA3 - 277

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase


Mass: 29895.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Gene: crtE, SYNPCC7002_A1085
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B1XJV9
#2: Protein Geranylgeranyl pyrophosphate synthase


Mass: 27777.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Gene: crtE, SYNPCC7002_A1085
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B1XJV9
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate (pH 4.6) and 30 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→68.816 Å / Num. obs: 24024 / % possible obs: 99.97 % / Redundancy: 1.99 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03119 / Rpim(I) all: 0.3119 / Rrim(I) all: 0.0441 / Net I/σ(I): 11.72
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.4474 / Num. unique obs: 2358 / CC1/2: 0.776 / Rpim(I) all: 0.4474 / Rrim(I) all: 0.6327

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e8h

5e8h


Resolution: 2.5→68.82 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.476 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.324
RfactorNum. reflection% reflectionSelection details
Rfree0.3057 1205 5 %RANDOM
Rwork0.24264 ---
obs0.24589 22819 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.39 Å2
Baniso -1Baniso -2Baniso -3
1-5.53 Å2-0 Å2-0 Å2
2---2.34 Å2-0 Å2
3----3.19 Å2
Refinement stepCycle: 1 / Resolution: 2.5→68.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 10 29 3963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123978
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.6265407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4655528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42323.391174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.08415645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6221520
X-RAY DIFFRACTIONr_chiral_restr0.1250.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022952
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.1917.682132
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.87611.4782653
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.9897.8431846
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined17.7466192
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7366 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 85 -
Rwork0.342 1667 -
obs--99.94 %

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