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- PDB-7my1: Sy-CrtE structure with IPP, N-term His-tag -

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Basic information

Entry
Database: PDB / ID: 7my1
TitleSy-CrtE structure with IPP, N-term His-tag
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / Prenyl transferase / Isopentenyl pyrophosphate / Dimethylallyl pyrophosphate / cyanobacteria / terpenoids
Function / homology
Function and homology information


dimethylallyltranstransferase / prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
: / : / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / dimethylallyltranstransferase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPeat, T.S. / Newman, J.
CitationJournal: Febs J. / Year: 2022
Title: Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase.
Authors: Satta, A. / Esquirol, L. / Ebert, B.E. / Newman, J. / Peat, T.S. / Plan, M. / Schenk, G. / Vickers, C.E.
History
DepositionMay 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0867
Polymers34,7071
Non-polymers3796
Water2,000111
1
AAA: Geranylgeranyl pyrophosphate synthase
hetero molecules

AAA: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,17314
Polymers69,4152
Non-polymers75812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5950 Å2
ΔGint-126 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.720, 73.261, 68.817
Angle α, β, γ (deg.)90.000, 109.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-601-

HOH

21AAA-609-

HOH

31AAA-611-

HOH

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase


Mass: 34707.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: crtE / Production host: Escherichia coli (E. coli) / References: UniProt: P72683
#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein was at 10 mg/mL and the drops were 200 nL plus 200 nL with the reservoir being 22.5% PEG 3350, 0.3M MgCl2, 0.1M Na-HEPES pH 6.55

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.84→45.16 Å / Num. obs: 24629 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Net I/σ(I): 9.4
Reflection shellResolution: 1.84→1.88 Å / Rmerge(I) obs: 1.367 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1295 / CC1/2: 0.574 / Rpim(I) all: 0.587 / % possible all: 85.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7mxz

7mxz


Resolution: 1.84→45.16 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.61 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2321 1160 4.711 %
Rwork0.1884 23465 -
all0.19 --
obs-24625 99.043 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.681 Å2-0 Å2-1.337 Å2
2--0.77 Å2-0 Å2
3----1.225 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 19 111 2227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132194
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172127
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6392991
X-RAY DIFFRACTIONr_angle_other_deg1.4551.5744888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3425288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29222.642106
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.104101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86315362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1621514
X-RAY DIFFRACTIONr_chiral_restr0.080.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_nbd_refined0.2240.2540
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21871
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21089
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2936
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2103
X-RAY DIFFRACTIONr_metal_ion_refined0.2110.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.210
X-RAY DIFFRACTIONr_nbd_other0.1960.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.214
X-RAY DIFFRACTIONr_mcbond_it2.5433.0071143
X-RAY DIFFRACTIONr_mcbond_other2.5443.0041142
X-RAY DIFFRACTIONr_mcangle_it3.5854.4981434
X-RAY DIFFRACTIONr_mcangle_other3.5844.5021435
X-RAY DIFFRACTIONr_scbond_it3.6353.5241051
X-RAY DIFFRACTIONr_scbond_other3.6163.5131045
X-RAY DIFFRACTIONr_scangle_it5.5945.1051557
X-RAY DIFFRACTIONr_scangle_other5.5925.1061558
X-RAY DIFFRACTIONr_lrange_it7.59858.4199546
X-RAY DIFFRACTIONr_lrange_other7.61258.4219475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.8850.36760.3351529X-RAY DIFFRACTION89.5647
1.885-1.9360.389850.3221688X-RAY DIFFRACTION99.8311
1.936-1.9920.37710.2861673X-RAY DIFFRACTION99.8855
1.992-2.0540.364850.2751587X-RAY DIFFRACTION99.9402
2.054-2.1210.299890.2531550X-RAY DIFFRACTION100
2.121-2.1950.333760.2481520X-RAY DIFFRACTION100
2.195-2.2780.251690.2181461X-RAY DIFFRACTION100
2.278-2.3710.245710.211395X-RAY DIFFRACTION99.9318
2.371-2.4760.22670.2051341X-RAY DIFFRACTION99.8582
2.476-2.5970.234640.2021281X-RAY DIFFRACTION100
2.597-2.7370.299620.1951218X-RAY DIFFRACTION100
2.737-2.9030.228670.1971160X-RAY DIFFRACTION100
2.903-3.1030.235470.1891091X-RAY DIFFRACTION99.9122
3.103-3.3510.247430.1871022X-RAY DIFFRACTION99.8126
3.351-3.670.165390.171948X-RAY DIFFRACTION99.5964
3.67-4.1010.23350.147847X-RAY DIFFRACTION99.7738
4.101-4.7330.14390.12748X-RAY DIFFRACTION99.1184
4.733-5.7890.206390.144629X-RAY DIFFRACTION99.1098
5.789-8.1540.145200.149504X-RAY DIFFRACTION99.2424
8.154-45.160.174160.133273X-RAY DIFFRACTION96.6555

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