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- PDB-5xn5: Homo-dimer crystal structure of geranylgeranyl diphosphate syntha... -

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Basic information

Entry
Database: PDB / ID: 5xn5
TitleHomo-dimer crystal structure of geranylgeranyl diphosphate synthases 1 from Oryza sativa
ComponentsOs07g0580900 protein
KeywordsTRANSFERASE / homo-dimer / lsu-lsu / OSGGPPS1
Function / homology
Function and homology information


geranylgeranyl diphosphate synthase activity / isoprenoid biosynthetic process / intracellular membrane-bounded organelle / 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
Os07g0580900 protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsWang, C. / Zhou, F. / Lu, S. / Zhang, P.
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 21, 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
B: Os07g0580900 protein


Theoretical massNumber of molelcules
Total (without water)65,7312
Polymers65,7312
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-43 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.022, 74.118, 71.288
Angle α, β, γ (deg.)90.000, 90.810, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 2 / 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 O103:H2 str. 12009 (bacteria)
References: UniProt: Q7XI92
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0 M sodium malonate, 20% PEG 3350, pH 7.0

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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: 2→38.1 Å / Num. obs: 39062 / % possible obs: 99.2 % / Redundancy: 4 % / Net I/σ(I): 19

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Processing

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

5e8h


Resolution: 2.002→38.056 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 1960 5.02 %
Rwork0.187 37091 -
obs0.1884 39051 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.89 Å2 / Biso mean: 33.0425 Å2 / Biso min: 16.84 Å2
Refinement stepCycle: final / Resolution: 2.002→38.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 0 226 4548
Biso mean---43.54 -
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114390
X-RAY DIFFRACTIONf_angle_d1.3745955
X-RAY DIFFRACTIONf_chiral_restr0.066685
X-RAY DIFFRACTIONf_plane_restr0.007780
X-RAY DIFFRACTIONf_dihedral_angle_d13.7871605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0022-2.05230.31491290.25022423255292
2.0523-2.10780.29271530.228926592812100
2.1078-2.16980.2561300.212826532783100
2.1698-2.23980.21191090.205627042813100
2.2398-2.31990.25751670.195226272794100
2.3199-2.41270.25791200.19426452765100
2.4127-2.52250.20211350.193826852820100
2.5225-2.65550.21481510.196526672818100
2.6555-2.82180.22441400.18726552795100
2.8218-3.03960.20571420.190626552797100
3.0396-3.34530.19341290.178626932822100
3.3453-3.8290.17831520.175826602812100
3.829-4.82260.19471590.159426772836100
4.8226-38.06290.21681440.19072688283298
Refinement TLS params.Method: refined / Origin x: 14.9781 Å / Origin y: 12.9069 Å / Origin z: 19.2809 Å
111213212223313233
T0.1246 Å20.0008 Å20.002 Å2-0.1932 Å2-0.0044 Å2--0.1573 Å2
L0.3052 °20.2077 °2-0.0582 °2-2.0448 °2-0.6824 °2--0.5454 °2
S-0.0003 Å °0.0385 Å °-0.0157 Å °-0.0731 Å °-0.0226 Å °-0.1419 Å °0.0388 Å °-0.0026 Å °0.0196 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 305
2X-RAY DIFFRACTION1allB3 - 305
3X-RAY DIFFRACTION1allS1 - 266

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