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- PDB-1wmw: Crystal structure of geranulgeranyl diphosphate synthase from The... -

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Basic information

Entry
Database: PDB / ID: 1wmw
TitleCrystal structure of geranulgeranyl diphosphate synthase from Thermus thermophilus
Componentsgeranylgeranyl diphosphate synthetase
KeywordsTRANSFERASE / GGPP / PRENYL DIPHOSPHATE SYNTHASE / THERMUS / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


geranylgeranyl diphosphate biosynthetic process / farnesyltranstransferase activity
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
Geranylgeranyl diphosphate synthetase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsSuto, K. / Nishio, K. / Nodake, Y. / Hamada, K. / Kawamoto, M. / Nakagawa, N. / Kuramitu, S. / Miura, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: To be Published
Title: Crystal structure of geranulgeranyl diphosphate synthase from Thermus thermophilus
Authors: Suto, K. / Nishio, K. / Nodake, Y. / Hamada, K. / Kawamoto, M. / Nakagawa, N. / Kuramitu, S. / Miura, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Expression, purification, crystallization and preliminary X-ray studies of geranylgeranyl diphosphate synthase from Thermus thermophilus HB8
Authors: Nishio, K. / Nodake, Y. / Hamada, K. / Suto, K. / Nakagawa, N. / Kuramitsu, S. / Miura, K.
History
DepositionJul 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 diphosphate synthetase
B: geranylgeranyl diphosphate synthetase
C: geranylgeranyl diphosphate synthetase
D: geranylgeranyl diphosphate synthetase


Theoretical massNumber of molelcules
Total (without water)146,2084
Polymers146,2084
Non-polymers00
Water21,3841187
1
A: geranylgeranyl diphosphate synthetase
B: geranylgeranyl diphosphate synthetase


Theoretical massNumber of molelcules
Total (without water)73,1042
Polymers73,1042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-26 kcal/mol
Surface area24870 Å2
MethodPISA
2
C: geranylgeranyl diphosphate synthetase
D: geranylgeranyl diphosphate synthetase


Theoretical massNumber of molelcules
Total (without water)73,1042
Polymers73,1042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-27 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.880, 139.880, 73.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
geranylgeranyl diphosphate synthetase


Mass: 36552.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5SMD0, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1187 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.97880, 0.97777, 0.97760, 0.96860
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 28, 2000
RadiationMonochromator: SILICON / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.977771
30.97761
40.96861
ReflectionResolution: 1.55→30 Å / Num. all: 204955 / Num. obs: 182752 / % possible obs: 89.2 % / Observed criterion σ(F): 5.58 / Observed criterion σ(I): 40.73 / Redundancy: 3.3 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.039
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.115 / % possible all: 81.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→19.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2726389.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 9157 5 %RANDOM
Rwork0.175 ---
obs0.175 182688 89 %-
all-204846 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0057 Å2 / ksol: 0.378019 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2---0.87 Å20 Å2
3---1.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.06 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10139 0 0 1187 11326
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.182 1442 5.1 %
Rwork0.159 26827 -
obs--83.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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