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- PDB-6sxn: Crystal structure of P212121 apo form of CrtE -

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Basic information

Entry
Database: PDB / ID: 6sxn
TitleCrystal structure of P212121 apo form of CrtE
Components(Geranylgeranyl pyrophosphate ...) x 6
KeywordsTRANSFERASE / Isoprenoid / prenyltransferase
Function / homology
Function and homology information


geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / geranylgeranyl diphosphate synthase activity / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase 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 ...: / : / 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
Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
C: Geranylgeranyl pyrophosphate synthase
D: Geranylgeranyl pyrophosphate synthase
E: Geranylgeranyl pyrophosphate synthase
F: Geranylgeranyl pyrophosphate synthase


Theoretical massNumber of molelcules
Total (without water)168,3706
Polymers168,3706
Non-polymers00
Water82946
1
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase


Theoretical massNumber of molelcules
Total (without water)56,6122
Polymers56,6122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-40 kcal/mol
Surface area22500 Å2
MethodPISA
2
C: Geranylgeranyl pyrophosphate synthase
E: Geranylgeranyl pyrophosphate synthase


Theoretical massNumber of molelcules
Total (without water)55,6862
Polymers55,6862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-40 kcal/mol
Surface area21510 Å2
MethodPISA
3
D: Geranylgeranyl pyrophosphate synthase
F: Geranylgeranyl pyrophosphate synthase


Theoretical massNumber of molelcules
Total (without water)56,0722
Polymers56,0722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-42 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.555, 122.973, 134.185
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
11F
21A
12F
22B
13F
23C
14F
24D
15F
25E
16A
26B
17A
27C
18A
28D
19A
29E
110B
210C
111B
211D
112B
212E
113C
213D
114C
214E
115D
215E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010F9 - 297
2010A9 - 297
1020F9 - 297
2020B9 - 297
1030F9 - 297
2030C9 - 297
1040F9 - 300
2040D9 - 300
1050F9 - 300
2050E9 - 300
1060A9 - 297
2060B9 - 297
1070A9 - 297
2070C9 - 297
1080A9 - 297
2080D9 - 297
1090A9 - 297
2090E9 - 297
10100B9 - 297
20100C9 - 297
10110B9 - 297
20110D9 - 297
10120B9 - 297
20120E9 - 297
10130C9 - 297
20130D9 - 297
10140C9 - 297
20140E9 - 297
10150D9 - 299
20150E9 - 299

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Geranylgeranyl pyrophosphate ... , 6 types, 6 molecules ABCDEF

#1: Protein Geranylgeranyl pyrophosphate synthase


Mass: 28720.965 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: 27891.006 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: Protein Geranylgeranyl pyrophosphate synthase


Mass: 27830.996 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
#4: Protein Geranylgeranyl pyrophosphate synthase


Mass: 28795.043 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
#5: Protein Geranylgeranyl pyrophosphate synthase


Mass: 27855.023 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
#6: Protein Geranylgeranyl pyrophosphate synthase


Mass: 27277.283 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

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Non-polymers , 1 types, 46 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.658→68.017 Å / Num. obs: 49329 / % possible obs: 99.24 % / Redundancy: 1.99 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05602 / Rpim(I) all: 0.05602 / Rrim(I) all: 0.07922 / Net I/σ(I): 11.76
Reflection shellResolution: 2.66→2.75 Å / Rmerge(I) obs: 0.7539 / Num. unique obs: 4674 / CC1/2: 0.806 / Rpim(I) all: 0.7539 / Rrim(I) all: 1.066

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e8h

5e8h


Resolution: 2.66→68.02 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.96 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R: 1.839 / ESU R Free: 0.381
RfactorNum. reflection% reflectionSelection details
Rfree0.2849 2407 4.9 %RANDOM
Rwork0.22795 ---
obs0.23075 46759 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.932 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å2-0 Å2
2---1.64 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.66→68.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11321 0 0 46 11367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01211460
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.62515576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45251544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12623.319476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.958151823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2421554
X-RAY DIFFRACTIONr_chiral_restr0.1350.21602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028531
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_it8.4946.8166233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.38310.1797758
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.6367.2465227
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined19.23793.78617551
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11F77770.07
12A77770.07
21F77170.07
22B77170.07
31F78110.08
32C78110.08
41F75390.07
42D75390.07
51F77240.07
52E77240.07
61A77440.06
62B77440.06
71A78660.06
72C78660.06
81A75800.06
82D75800.06
91A76870.07
92E76870.07
101B77810.07
102C77810.07
111B75280.07
112D75280.07
121B76170.08
122E76170.08
131C75710.06
132D75710.06
141C76730.07
142E76730.07
151D75880.07
152E75880.07
LS refinement shellResolution: 2.66→2.727 Å
RfactorNum. reflection% reflection
Rfree0.427 172 -
Rwork0.352 3225 -
obs--93.92 %

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