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- PDB-2dh4: Geranylgeranyl pyrophosphate synthase -

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Basic information

Entry
Database: PDB / ID: 2dh4
TitleGeranylgeranyl pyrophosphate synthase
ComponentsYPL069C
KeywordsTRANSFERASE / alpha helix / prenyl transferase / pyrophosphate
Function / homology
Function and homology information


Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity ...Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / terpenoid biosynthetic process / isoprenoid biosynthetic process / protein transport / mitochondrion / metal ion binding
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 pyrophosphate synthase BTS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD with data collected on Se-Met crystal at 0.9796 A. / Resolution: 1.98 Å
AuthorsChang, T.-H. / Guo, R.-T. / Ko, T.-P. / Wang, A.H. / Liang, P.-H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of Type-III Geranylgeranyl Pyrophosphate Synthase from Saccharomyces cerevisiae and the Mechanism of Product Chain Length Determination.
Authors: Chang, T.-H. / Guo, R.-T. / Ko, T.-P. / Wang, A.H. / Liang, P.-H.
History
DepositionMar 22, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YPL069C
B: YPL069C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6474
Polymers78,5982
Non-polymers492
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-66 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.747, 116.331, 129.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit and biological unit is a dimer.

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Components

#1: Protein YPL069C / geranylgeranyl pyrophosphate synthase


Mass: 39299.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GGPPS / Plasmid: pET32 Xa/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q12051, geranylgeranyl diphosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25mM Tris-HCl, 150mM NaCl, 0.1% Triton X-100, 80mM Na-acetate, 145mM ammonium sulphate, 13% PEG 4000, 8% propanediol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B211.0332, 0.9799, 0.9796, 0.9537
SYNCHROTRONNSRRC BL17B221.1274
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 4, 2005
MAR scanner 345 mm plate2IMAGE PLATEMar 21, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.97991
30.97961
40.95371
51.12741
ReflectionResolution: 1.98→50 Å / Num. all: 52304 / Num. obs: 50750 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 28
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5175 / % possible all: 82.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: SAD with data collected on Se-Met crystal at 0.9796 A.
Resolution: 1.98→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2373 -RANDOM
Rwork0.189 ---
all0.192 52304 --
obs0.192 47348 90.5 %-
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5320 0 2 578 5900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.66
LS refinement shellResolution: 1.98→2.05 Å / Rfactor Rfree error: 0.051
RfactorNum. reflection% reflection
Rfree0.357 184 -
Rwork0.306 --
obs-3544 68.5 %

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