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- PDB-3apz: Apo form of Arabidopsis medium/long-chain length prenyl pyrophosp... -

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Basic information

Entry
Database: PDB / ID: 3apz
TitleApo form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase
ComponentsGeranyl diphosphate synthase
KeywordsTRANSFERASE / prenyltransferase / All alpha-helices fold / chroloplast / isoprenoid biosynthetic process
Function / homology
Function and homology information


all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific] / all-trans-nonaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific) activity / ubiquinone biosynthetic process / embryo development ending in seed dormancy / prenyltransferase activity / plastid / isoprenoid biosynthetic process / chloroplast / 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
Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial / Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsHsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J.
CitationJournal: Plant Physiol. / Year: 2011
Title: Structure and mechanism of an Arabidopsis medium/long-chain-length prenyl pyrophosphate synthase
Authors: Hsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J.
History
DepositionOct 24, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geranyl diphosphate synthase
B: Geranyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)76,1512
Polymers76,1512
Non-polymers00
Water6,720373
1
A: Geranyl diphosphate synthase

A: Geranyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)76,1512
Polymers76,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+1/2,y,-z+1/21
Buried area2650 Å2
ΔGint-25 kcal/mol
Surface area28740 Å2
MethodPISA
2
B: Geranyl diphosphate synthase

B: Geranyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)76,1512
Polymers76,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area2480 Å2
ΔGint-27 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.512, 150.126, 176.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Geranyl diphosphate synthase


Mass: 38075.535 Da / Num. of mol.: 2 / Fragment: residues in UNP 76-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AtNPPPS, gpps / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9FT89, UniProt: Q5HZ00*PLUS, heptaprenyl diphosphate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 60%(v/v) Tacsimate, pH 7.0, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 27, 2009
RadiationMonochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 33211 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10427 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WY0

1wy0


Resolution: 2.6→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8107 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1371 4.5 %RANDOM
Rwork0.2064 ---
obs-28230 93.1 %-
Solvent computationBsol: 34.3958 Å2
Displacement parametersBiso max: 128.26 Å2 / Biso mean: 48.9747 Å2 / Biso min: 12.27 Å2
Baniso -1Baniso -2Baniso -3
1-11.271 Å20 Å20 Å2
2---11.27 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 0 373 4959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4741.5
X-RAY DIFFRACTIONc_scbond_it2.1652
X-RAY DIFFRACTIONc_mcangle_it2.5912
X-RAY DIFFRACTIONc_scangle_it3.4262.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.630.3254520.3129810862
2.63-2.670.3379480.3157862910
2.67-2.70.4589490.3133897946
2.7-2.740.3569390.2951893932
2.74-2.780.3376450.2705916961
2.78-2.830.2452350.2565949984
2.83-2.870.295510.2527940991
2.87-2.920.3227470.2571949996
2.92-2.980.2176570.2342931988
2.98-3.030.3255520.25229701022
3.03-3.090.2949560.24829641020
3.09-3.160.3832460.25879931039
3.16-3.240.3573520.24649971049
3.24-3.320.2787590.236310291088
3.32-3.410.3031430.201110121055
3.41-3.510.2675580.184510241082
3.51-3.620.2167660.167110241090
3.62-3.750.2415580.17610391097
3.75-3.90.2328480.1810461094
3.9-4.070.2019450.164910611106
4.07-4.290.2116510.160110881139
4.29-4.560.1948600.14210501110
4.56-4.910.1911410.158110751116
4.91-5.40.2235610.186310691130
5.4-6.170.3457570.245510651122
6.17-7.760.2691490.221811011150
7.76-300.1843460.205211051151
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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