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- PDB-3lji: CRYSTAL STRUCTURE OF putative geranyltranstransferase from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 3lji
TitleCRYSTAL STRUCTURE OF putative geranyltranstransferase from Pseudomonas fluorescens Pf-5
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Isoprene biosynthesis / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


(2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / isoprenoid biosynthetic process / 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
Geranyltranstransferase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsMalashkevich, V.N. / Toro, R. / Patskovsky, Y. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative geranyltranstransferase from Pseudomonas fluorescens Pf-5
Authors: Malashkevich, V.N. / Toro, R. / Patskovsky, Y. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 21, 2018Group: Data collection / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranyltranstransferase


Theoretical massNumber of molelcules
Total (without water)32,9101
Polymers32,9101
Non-polymers00
Water4,972276
1
A: Geranyltranstransferase

A: Geranyltranstransferase


Theoretical massNumber of molelcules
Total (without water)65,8202
Polymers65,8202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3530 Å2
ΔGint-33 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.639, 48.340, 75.693
Angle α, β, γ (deg.)90.000, 121.220, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

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Components

#1: Protein Geranyltranstransferase /


Mass: 32910.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: PFL_5509 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q4K5A6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG MME, 150 mM potassium bromide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 99504 / % possible obs: 96.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Χ2: 0.772 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.39-1.412.70.48940750.533179.8
1.41-1.4430.47348330.548192.6
1.44-1.473.10.36749160.593195.4
1.47-1.53.20.32349470.577196.2
1.5-1.533.20.28249920.586196.6
1.53-1.573.20.24249690.605196.7
1.57-1.63.20.21349900.63196.9
1.6-1.653.20.17750550.665197.1
1.65-1.73.20.14949700.686197.3
1.7-1.753.20.12850670.697197.6
1.75-1.813.20.10550440.725197.7
1.81-1.893.20.0950430.746197.9
1.89-1.973.20.07650880.845198.2
1.97-2.083.20.06550650.869198.4
2.08-2.213.20.05551380.912198.7
2.21-2.383.20.05450611.044198.8
2.38-2.623.20.05150981.108199.2
2.62-2.993.20.04551511.03199.3
2.99-3.7730.03751030.926198.9
3.77-503.20.03748990.974194.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.39→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.853 / SU B: 2.661 / SU ML: 0.048 / SU R Cruickshank DPI: 0.071 / SU Rfree: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2600 5.1 %RANDOM
Rwork0.202 ---
obs0.203 50973 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.53 Å2 / Biso mean: 19.746 Å2 / Biso min: 6.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.02 Å2
2--0.07 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 0 276 2300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222095
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9882851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3565283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67524.09188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99315346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1351515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211588
X-RAY DIFFRACTIONr_mcbond_it0.9653.51371
X-RAY DIFFRACTIONr_mcangle_it2.728502165
X-RAY DIFFRACTIONr_scbond_it5.6850724
X-RAY DIFFRACTIONr_scangle_it1.314.5679
LS refinement shellResolution: 1.391→1.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 183 -
Rwork0.303 3278 -
all-3461 -
obs--89.41 %
Refinement TLS params.Method: refined / Origin x: 33.0311 Å / Origin y: 35.1869 Å / Origin z: 12.3123 Å
111213212223313233
T0.0334 Å2-0.0012 Å20.0002 Å2-0.0316 Å20.0215 Å2--0.0228 Å2
L0.6785 °2-0.0013 °2-0.2283 °2-0.269 °20.3354 °2--0.7013 °2
S0.0273 Å °-0.0661 Å °-0.041 Å °0.0214 Å °0.002 Å °-0.0084 Å °0.0364 Å °-0.0453 Å °-0.0293 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 293
2X-RAY DIFFRACTION1A305 - 580

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