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- PDB-4wk5: Crystal structure of a Isoprenoid Synthase family member from The... -

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Basic information

Entry
Database: PDB / ID: 4wk5
TitleCrystal structure of a Isoprenoid Synthase family member from Thermotoga neapolitana DSM 4359, target EFI-509458
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / Isoprenoid Synthase / enzyme function initiative / EFI / Structural Genomics
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 speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsToro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. ...Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Poulter, C.D. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of a Isoprenoid Synthase family member from Thermotoga neapolitana DSM 4359, target EFI-509458
Authors: Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / ...Authors: Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Poulter, C.D. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)33,4841
Polymers33,4841
Non-polymers00
Water2,810156
1
A: Geranyltranstransferase

A: Geranyltranstransferase


Theoretical massNumber of molelcules
Total (without water)66,9672
Polymers66,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3600 Å2
ΔGint-43 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.223, 118.458, 79.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21A-333-

HOH

31A-358-

HOH

Detailsbiological unit is a dimer

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Components

#1: Protein Geranyltranstransferase / / Isoprenoid Synthase


Mass: 33483.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Strain: DSM 4359 / Gene: CTN_0526 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9K6W9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Protein (24.6 mg/ml, 10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol); Reservoir (0.8 M Ammonium Sulfate, 0.1 M tri-Sodium Citrate pH 4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 14, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 37530 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 23.66 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Χ2: 1.763 / Net I/av σ(I): 37.904 / Net I/σ(I): 9.4 / Num. measured all: 274712
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.7-1.737.30.97518260.7610.3881.361100
1.73-1.767.30.84418430.8140.3371.3621000.909
1.76-1.797.30.73918490.8190.2951.4081000.797
1.79-1.837.30.59118770.8820.2351.3981000.637
1.83-1.877.40.50918490.9230.2021.4071000.548
1.87-1.917.30.40618430.9410.1611.4511000.437
1.91-1.967.40.34918540.9580.1381.4341000.376
1.96-2.027.40.27518690.9720.1081.4521000.296
2.02-2.077.40.20918600.9830.0821.4941000.224
2.07-2.147.40.16618530.9880.0661.5021000.179
2.14-2.227.40.13918880.9920.0551.491000.149
2.22-2.317.40.12718710.9930.051.5551000.136
2.31-2.417.40.11318630.9930.0451.7861000.121
2.41-2.547.40.11518790.9920.0462.2291000.124
2.54-2.77.20.10318750.9930.0422.4641000.111
2.7-2.917.20.09318920.9950.0382.7441000.1
2.91-3.27.30.0819030.9950.0322.81000.086
3.2-3.667.40.04919060.9980.0191.8881000.053
3.66-4.617.30.0419250.9990.0161.9091000.043
4.61-1006.90.04420050.9980.0192.10599.20.048

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→26.551 Å / FOM work R set: 0.8699 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 1754 4.68 %
Rwork0.1789 35749 -
obs0.1802 37503 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.71 Å2 / Biso mean: 33.04 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 1.7→26.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 0 156 2181
Biso mean---43.79 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072124
X-RAY DIFFRACTIONf_angle_d1.0112864
X-RAY DIFFRACTIONf_chiral_restr0.039317
X-RAY DIFFRACTIONf_plane_restr0.004372
X-RAY DIFFRACTIONf_dihedral_angle_d13.7797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6954-1.74120.27981290.24182515264493
1.7412-1.79250.26281400.218127252865100
1.7925-1.85030.20771390.206227512890100
1.8503-1.91640.22531350.193527362871100
1.9164-1.99310.1881340.185427302864100
1.9931-2.08380.19121190.17227552874100
2.0838-2.19360.20711340.159727372871100
2.1936-2.3310.19961470.167927302877100
2.331-2.51080.19821410.174727692910100
2.5108-2.76330.21961230.189427942917100
2.7633-3.16250.21391360.190427722908100
3.1625-3.98230.20451230.168528252948100
3.9823-26.55470.19711540.173329103064100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19490.0891-0.41620.55990.39530.5959-0.21420.15180.0582-0.51220.24110.00970.06040.1477-0.00070.2279-0.03890.0030.2283-0.01460.130510.57734.746520.7378
20.51580.07830.40120.71770.29620.7105-0.06960.10460.1035-0.08830.102-0.0739-0.09790.04580.00010.183-0.03260.01440.1761-0.00860.166811.479110.019629.0753
30.46850.02180.44290.91540.19091.45-0.10810.0419-0.0699-0.03680.08720.0169-0.104-0.1476-0.00370.17420.01550.00810.16840.01050.10461.41134.178532.7481
40.11640.18850.11350.51880.0560.75460.0062-0.08730.2330.10780.1151-0.1486-0.10530.09470.00030.16470.0118-0.01470.1727-0.0020.168810.568.549445.1534
50.33520.44350.10121.40310.03540.7797-0.1277-0.09240.29790.28530.1156-0.0756-0.0940.0247-0.00270.22810.009-0.0250.1695-0.0210.216610.170117.806944.9646
60.7342-0.488-0.14610.8345-0.06610.4859-0.0048-0.09020.25540.20950.07640.0398-0.1359-0.0446-0.00020.21810.0095-0.0010.2012-0.0090.41186.604127.715341.2659
70.66610.2250.10150.59530.97311.7127-0.57770.30510.8875-0.60350.0341-0.2307-0.7028-0.0027-0.27490.3251-0.0536-0.06470.21770.06560.455316.481528.437829.3813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 74 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 120 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 144 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 183 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 252 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 253 through 268 )A0

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