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- PDB-2h8o: The 1.6A crystal structure of the geranyltransferase from Agrobac... -

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Basic information

Entry
Database: PDB / ID: 2h8o
TitleThe 1.6A crystal structure of the geranyltransferase from Agrobacterium tumefaciens
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / Geranyltransferase / Agrobacterium tumefaciens / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
Geranyltranstransferase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.6A crystal structure of the geranyltransferase from Agrobacterium tumefaciens
Authors: Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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: Geranyltranstransferase


Theoretical massNumber of molelcules
Total (without water)35,8161
Polymers35,8161
Non-polymers00
Water5,963331
1
A: Geranyltranstransferase

A: Geranyltranstransferase


Theoretical massNumber of molelcules
Total (without water)71,6322
Polymers71,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4650 Å2
ΔGint-44 kcal/mol
Surface area21880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.341, 79.807, 51.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThis protein existed as dimer. The second part of the biological assembly is generated by the two fold axis: -x+2, -y, z

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Components

#1: Protein Geranyltranstransferase /


Mass: 35816.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: ispA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8UBX7, UniProt: Q7CWE5*PLUS, (2E,6E)-farnesyl diphosphate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M NaH2PO4, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.6→51.85 Å / Num. all: 33621 / Num. obs: 33154 / % possible obs: 98.61 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 30.73
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.31 / Num. unique all: 2567 / % possible all: 86.99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→33.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.882 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.089 / ESU R Free: 0.084
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18804 1751 5 %RANDOM
Rwork0.16813 ---
all0.16914 33621 --
obs0.16914 33154 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.106 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--0.4 Å20 Å2
3---0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.031 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.6→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 0 331 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222164
X-RAY DIFFRACTIONr_bond_other_d0.0020.021461
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9862928
X-RAY DIFFRACTIONr_angle_other_deg0.91433571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.585291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00224.38898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12115379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4881519
X-RAY DIFFRACTIONr_chiral_restr0.0620.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
X-RAY DIFFRACTIONr_nbd_refined0.2290.2583
X-RAY DIFFRACTIONr_nbd_other0.1880.21602
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21095
X-RAY DIFFRACTIONr_nbtor_other0.0850.21095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.248
X-RAY DIFFRACTIONr_mcbond_it1.0051.51855
X-RAY DIFFRACTIONr_mcbond_other0.1811.5588
X-RAY DIFFRACTIONr_mcangle_it1.13322219
X-RAY DIFFRACTIONr_scbond_it2.3873819
X-RAY DIFFRACTIONr_scangle_it3.3854.5704
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 123 -
Rwork0.219 2110 -
obs-2233 86.99 %
Refinement TLS params.Method: refined / Origin x: 60.726 Å / Origin y: 15.267 Å / Origin z: 8.436 Å
111213212223313233
T-0.0658 Å2-0.0087 Å2-0.0064 Å2-0.0006 Å20.0218 Å2---0.0053 Å2
L0.8574 °2-0.0611 °2-0.0939 °2-1.3657 °2-0.1145 °2--0.1803 °2
S-0.0156 Å °0.0894 Å °0.2037 Å °0.113 Å °0.0116 Å °0.0364 Å °-0.0256 Å °0.005 Å °0.004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 7333 - 73
2X-RAY DIFFRACTION1AA74 - 11374 - 113
3X-RAY DIFFRACTION1AA114 - 153114 - 153
4X-RAY DIFFRACTION1AA154 - 200154 - 200
5X-RAY DIFFRACTION1AA201 - 250201 - 250
6X-RAY DIFFRACTION1AA251 - 290251 - 290
7X-RAY DIFFRACTION1AA291 - 332291 - 332

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