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- PDB-5xn6: Heterodimer crystal structure of geranylgeranyl diphosphate synth... -

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Basic information

Entry
Database: PDB / ID: 5xn6
TitleHeterodimer crystal structure of geranylgeranyl diphosphate synthases 1 with GGPPS Recruiting Protein(OsGRP) from Oryza sativa
Components
  • Os02g0668100 protein
  • Os07g0580900 protein
KeywordsTRANSFERASE / heterodimer / small-subunit / OsGGPPS1 / OsGRP
Function / homology
Function and homology information


geranylgeranyl diphosphate synthase activity / 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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Os02g0668100 protein / Os07g0580900 protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.598 Å
AuthorsWang, C. / Zhou, F. / Lu, S. / Zhang, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of science and technology of the people's republic of China#2013CB127004 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: A recruiting protein of geranylgeranyl diphosphate synthase controls metabolic flux toward chlorophyll biosynthesis in rice
Authors: Zhou, F. / Wang, C.Y. / Gutensohn, M. / Jiang, L. / Zhang, P. / Zhang, D. / Dudareva, N. / Lu, S.
History
DepositionMay 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 19, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 22, 2023Group: 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: Os07g0580900 protein
C: Os02g0668100 protein
B: Os07g0580900 protein
D: Os02g0668100 protein
E: Os07g0580900 protein
F: Os02g0668100 protein


Theoretical massNumber of molelcules
Total (without water)194,9806
Polymers194,9806
Non-polymers00
Water00
1
A: Os07g0580900 protein
C: Os02g0668100 protein


Theoretical massNumber of molelcules
Total (without water)64,9932
Polymers64,9932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-40 kcal/mol
Surface area23100 Å2
MethodPISA
2
B: Os07g0580900 protein
D: Os02g0668100 protein


Theoretical massNumber of molelcules
Total (without water)64,9932
Polymers64,9932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-37 kcal/mol
Surface area22510 Å2
MethodPISA
3
E: Os07g0580900 protein
F: Os02g0668100 protein


Theoretical massNumber of molelcules
Total (without water)64,9932
Polymers64,9932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-35 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.062, 102.981, 103.486
Angle α, β, γ (deg.)109.390, 109.590, 109.130
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Os07g0580900 protein / Putative geranylgeranyl diphosphate synthase / cDNA clone:J023007O22 / full insert sequence / cDNA ...Putative geranylgeranyl diphosphate synthase / cDNA clone:J023007O22 / full insert sequence / cDNA clone:J033030K23


Mass: 32865.441 Da / Num. of mol.: 3 / Fragment: UNP residues 62-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os07g0580900, OJ1301_C12.3, OSNPB_070580900, P0453G03.27
Production host: Escherichia coli 536 (bacteria) / References: UniProt: Q7XI92
#2: Protein Os02g0668100 protein / Putative geranylgeranyl diphosphate synthase / cDNA clone:001-204-C07 / full insert sequence / cDNA ...Putative geranylgeranyl diphosphate synthase / cDNA clone:001-204-C07 / full insert sequence / cDNA clone:002-182-E03 / cDNA clone:J023091L04


Mass: 32127.785 Da / Num. of mol.: 3 / Fragment: UNP residues 39-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os02g0668100, OJ1725_H08.13, OSNPB_020668100
Production host: Escherichia coli O103:H2 str. 12009 (bacteria)
References: UniProt: Q6ET88

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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: 4.35 Å3/Da / Density % sol: 71.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 16% PEG 10000, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9798 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Sep 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.59→37.8 Å / Num. obs: 36920 / % possible obs: 96.9 % / Redundancy: 1.9 % / Net I/σ(I): 8.26

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
HKL-2000data reduction
HKL-2000data reduction
HKL-2000data reduction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E8H

5e8h


Resolution: 3.598→37.755 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1845 5 %
Rwork0.2519 35036 -
obs0.2525 36881 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.48 Å2 / Biso mean: 90.3147 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.598→37.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12244 0 0 0 12244
Num. residues----1627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312614
X-RAY DIFFRACTIONf_angle_d2.54217118
X-RAY DIFFRACTIONf_chiral_restr0.131977
X-RAY DIFFRACTIONf_plane_restr0.0122240
X-RAY DIFFRACTIONf_dihedral_angle_d16.2814588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5976-3.69480.37471290.36852446257589
3.6948-3.80340.31661630.3492710287397
3.8034-3.9260.3661660.32622688285497
3.926-4.06620.31841200.30332733285398
4.0662-4.22880.3211230.30112736285997
4.2288-4.4210.28851410.28712741288298
4.421-4.65370.26021300.25562703283397
4.6537-4.94460.28591450.24942779292498
4.9446-5.32550.30791410.27642683282497
5.3255-5.85960.29691360.29652683281997
5.8596-6.70340.28651450.28642673281896
6.7034-8.430.21621450.19372773291899
8.43-37.75690.17511610.16262688284997
Refinement TLS params.Method: refined / Origin x: 17.4289 Å / Origin y: 91.8222 Å / Origin z: 84.0313 Å
111213212223313233
T0.6796 Å20.0447 Å2-0.0119 Å2-0.7516 Å2-0.0364 Å2--0.6788 Å2
L0.2988 °20.0329 °2-0.043 °2-0.3854 °2-0.2554 °2--0.5771 °2
S0.0369 Å °-0.0048 Å °0.0163 Å °-0.0382 Å °-0.0064 Å °0.0674 Å °0.0797 Å °0.0178 Å °-0.0321 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 305
2X-RAY DIFFRACTION1allC4 - 289
3X-RAY DIFFRACTION1allB3 - 305
4X-RAY DIFFRACTION1allD3 - 289
5X-RAY DIFFRACTION1allE3 - 305
6X-RAY DIFFRACTION1allF3 - 288

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