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- PDB-7mxz: Sy-CrtE apo structure -

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Basic information

Entry
Database: PDB / ID: 7mxz
TitleSy-CrtE apo structure
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / Prenyl transferase / Isopentenyl pyrophosphate / Dimethylallyl pyrophosphate / cyanobacteria / terpenoids
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding
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
Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
AAA: Geranylgeranyl pyrophosphate synthase
BBB: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0967
Polymers66,9522
Non-polymers1445
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-74 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.497, 73.650, 132.172
Angle α, β, γ (deg.)90.000, 95.675, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-600-

HOH

21BBB-710-

HOH

31BBB-776-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 7 - 304 / Label seq-ID: 7 - 304

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase


Mass: 33476.082 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Droplets were 200 nL protein at 10 mg/mL plus 200 nL reservoir, 0.2 M MgCl2 and 20 %(w/v) PEG 3350.

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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: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.47→43.84 Å / Num. obs: 98723 / % possible obs: 98.2 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Net I/σ(I): 10.5
Reflection shellResolution: 1.47→1.49 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.805 / Num. unique obs: 4443 / CC1/2: 0.885 / Rpim(I) all: 0.334 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kro

3kro


Resolution: 1.47→39.763 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.22 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1847 4987 5.056 %
Rwork0.1604 93648 -
all0.162 --
obs-98635 98.148 %
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: 18.078 Å2
Baniso -1Baniso -2Baniso -3
1-1.868 Å20 Å20.121 Å2
2---1.377 Å20 Å2
3----0.505 Å2
Refinement stepCycle: LAST / Resolution: 1.47→39.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4313 0 5 558 4876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134624
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174491
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.6386321
X-RAY DIFFRACTIONr_angle_other_deg1.6231.57510349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5375623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19122.793222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34215784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6381529
X-RAY DIFFRACTIONr_chiral_restr0.1020.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
X-RAY DIFFRACTIONr_nbd_refined0.2350.21113
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.24110
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22382
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2359
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.214
X-RAY DIFFRACTIONr_nbd_other0.1790.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.240
X-RAY DIFFRACTIONr_mcbond_it1.7181.6062423
X-RAY DIFFRACTIONr_mcbond_other1.7161.6042422
X-RAY DIFFRACTIONr_mcangle_it2.5122.3943069
X-RAY DIFFRACTIONr_mcangle_other2.5122.3963070
X-RAY DIFFRACTIONr_scbond_it3.0792.0162201
X-RAY DIFFRACTIONr_scbond_other3.0782.0172202
X-RAY DIFFRACTIONr_scangle_it4.7412.8673252
X-RAY DIFFRACTIONr_scangle_other4.742.8673252
X-RAY DIFFRACTIONr_lrange_it5.73632.12320611
X-RAY DIFFRACTIONr_lrange_other5.65831.57420090
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.059221
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.083630.05006
12BBBX-RAY DIFFRACTIONLocal ncs0.083630.05006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.5040.263640.2436511X-RAY DIFFRACTION92.3191
1.504-1.5450.2243650.2136666X-RAY DIFFRACTION97.7886
1.545-1.590.2133640.1956454X-RAY DIFFRACTION97.7491
1.59-1.6390.1953630.1826309X-RAY DIFFRACTION97.8586
1.639-1.6930.1933250.1756166X-RAY DIFFRACTION98.438
1.693-1.7520.2183000.1736011X-RAY DIFFRACTION98.241
1.752-1.8180.2042970.175827X-RAY DIFFRACTION98.822
1.818-1.8920.2013110.1625502X-RAY DIFFRACTION98.6257
1.892-1.9770.2142540.1655436X-RAY DIFFRACTION99.2153
1.977-2.0730.1852620.1535159X-RAY DIFFRACTION99.1405
2.073-2.1850.1592550.1474911X-RAY DIFFRACTION99.308
2.185-2.3180.1522700.1394572X-RAY DIFFRACTION99.3638
2.318-2.4780.1741970.1384418X-RAY DIFFRACTION99.4398
2.478-2.6760.1742390.1414058X-RAY DIFFRACTION99.4676
2.676-2.9310.1791880.1513740X-RAY DIFFRACTION99.3173
2.931-3.2770.1841890.1583357X-RAY DIFFRACTION98.8019
3.277-3.7840.1681660.1582961X-RAY DIFFRACTION98.3024
3.784-4.6330.1481220.1392526X-RAY DIFFRACTION98.4021
4.633-6.5480.2121050.1811965X-RAY DIFFRACTION98.0578
6.548-39.7630.227510.1881099X-RAY DIFFRACTION96.6387

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