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- PDB-1wy0: Crystal structure of geranylgeranyl pyrophosphate synthetase from... -

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Basic information

Entry
Database: PDB / ID: 1wy0
TitleCrystal structure of geranylgeranyl pyrophosphate synthetase from Pyrococcus horikoshii Ot3
Componentsgeranylgeranyl pyrophosphate synthetase
KeywordsTRANSFERASE / geranylgeranyl pyrophosphate synthetase / Pyrococcus horikoshii / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / PH1072
Function / homology
Function and homology information


isoprenoid biosynthetic process / transferase 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
BROMIDE ION / : / : / 342aa long hypothetical geranylgeranyl pyrophosphate synthetase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.2 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of geranylgeranyl pyrophosphate synthetase from Pyrococcus horikoshii Ot3
Authors: Sugahara, M. / Kunishima, N.
History
DepositionFeb 3, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / 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_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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: geranylgeranyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8933
Polymers38,6131
Non-polymers2802
Water3,189177
1
A: geranylgeranyl pyrophosphate synthetase
hetero molecules

A: geranylgeranyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7866
Polymers77,2252
Non-polymers5614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3910 Å2
ΔGint-85 kcal/mol
Surface area27280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.353, 75.780, 80.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer in the asymmetric unit by the operations: -x, -y, z.

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Components

#1: Protein geranylgeranyl pyrophosphate synthetase


Mass: 38612.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: GenBank: 14590908, UniProt: O58799*PLUS
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.5 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.8
Details: JAM-600, DTT, NaBr, EMTS, pH 4.8, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 7, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 20465 / Num. obs: 20465 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 41.376 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.087 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1995 / Rsym value: 0.471 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→14.9 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 986 -RANDOM
Rwork0.246 ---
obs0.246 20293 100 %-
all-20293 --
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å20 Å2
2---2.8 Å20 Å2
3----0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 2 177 2774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.313 107 -
Rwork0.288 --
obs-1878 100 %

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