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- PDB-4f62: Crystal structure of a putative farnesyl-diphosphate synthase fro... -

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Basic information

Entry
Database: PDB / ID: 4f62
TitleCrystal structure of a putative farnesyl-diphosphate synthase from Marinomonas sp. MED121 (Target EFI-501980)
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / Enzyme Function Initiative / Structural Genomics
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / cytoplasm
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 speciesMarinomonas sp. MED121 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
Authors: Wallrapp, F.H. / Pan, J.J. / Ramamoorthy, G. / Almonacid, D.E. / Hillerich, B.S. / Seidel, R. / Patskovsky, Y. / Babbitt, P.C. / Almo, S.C. / Jacobson, M.P. / Poulter, C.D.
History
DepositionMay 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Nov 15, 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 1.4Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Geranyltranstransferase
B: Geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5236
Polymers70,2072
Non-polymers3164
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-63 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.491, 96.491, 156.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Geranyltranstransferase / isoprenoid synthase


Mass: 35103.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas sp. MED121 (bacteria) / Gene: MED121_18165 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A3YCB7, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein: 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM magnesium chloride, reservoir: 0.1 M sodium chloride, 0.1 M HEPES, pH 7.5, 1.6 M ammonium sulfate, ...Details: protein: 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM magnesium chloride, reservoir: 0.1 M sodium chloride, 0.1 M HEPES, pH 7.5, 1.6 M ammonium sulfate, cryoprotectant: reservoir + 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2011 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 49760 / Num. obs: 49760 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.076 / Χ2: 1.319 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1411.70.75124701.0571100
2.14-2.1811.70.65924361.0861100
2.18-2.2211.70.59124471.1331100
2.22-2.2611.60.51824551.2741100
2.26-2.3111.80.46624461.1971100
2.31-2.3711.80.37824631.31100
2.37-2.4211.90.32424641.331100
2.42-2.4911.80.27624661.4011100
2.49-2.5611.90.23624541.4731100
2.56-2.6511.90.19824591.5161100
2.65-2.7411.80.17625031.6951100
2.74-2.8511.90.14424721.5651100
2.85-2.9811.90.11724711.5471100
2.98-3.1411.90.124871.4381100
3.14-3.33120.08624891.3041100
3.33-3.5911.90.0825071.2751100
3.59-3.9511.80.07224961.4651100
3.95-4.5211.80.05625391.3161100
4.52-5.711.50.0425610.963199.9
5.7-5011.40.03426751.038199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LSN

3lsn


Resolution: 2.101→41.059 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.862 / SU ML: 0.21 / σ(F): 0 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 1897 4.01 %RANDOM
Rwork0.1771 ---
all0.1782 47352 --
obs0.1782 47352 95.19 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.814 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 132.89 Å2 / Biso mean: 53.5003 Å2 / Biso min: 26.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.3175 Å2-0 Å20 Å2
2---3.3175 Å20 Å2
3---6.6351 Å2
Refinement stepCycle: LAST / Resolution: 2.101→41.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3985 0 18 157 4160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074082
X-RAY DIFFRACTIONf_angle_d1.0125522
X-RAY DIFFRACTIONf_chiral_restr0.065650
X-RAY DIFFRACTIONf_plane_restr0.005712
X-RAY DIFFRACTIONf_dihedral_angle_d14.6241497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.101-2.15390.24691230.21453023314690
2.1539-2.21210.26551280.20023008313690
2.2121-2.27720.20321180.18773025314390
2.2772-2.35070.22391280.18863113324192
2.3507-2.43470.20261310.19023118324993
2.4347-2.53210.2931350.19483171330694
2.5321-2.64740.23111400.19483198333895
2.6474-2.78690.22081370.19413280341796
2.7869-2.96150.24681370.19763276341397
2.9615-3.19010.23241410.19443338347998
3.1901-3.51090.24271410.18363395353699
3.5109-4.01860.17231480.163834323580100
4.0186-5.06150.16561430.144434693612100
5.0615-41.06710.17711470.178536093756100
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)
11.87360.11511.1731.59010.52354.810.07660.1885-0.46310.03970.0005-0.10270.4883-0.1846-0.08450.17970.0064-0.03790.2834-0.12510.334726.888232.485337.9775
24.2132-0.28150.85731.21440.27111.3017-0.06480.1488-0.0694-0.00750.04450.0665-0.0056-0.1270.04480.27280.031-0.03730.3849-0.08090.316811.77244.101530.9979
34.40171.15562.60191.1610.25813.3518-0.4812-0.70981.26680.4524-0.25630.422-0.5694-0.52260.66830.520.1269-0.14690.4458-0.22020.535130.600656.038657.5983
48.59550.7503-2.15932.9613-1.15024.2438-0.0103-0.44590.69880.2616-0.2552-0.0716-0.9280.26760.26380.4743-0.0231-0.18610.3503-0.05510.366242.959751.756158.8931
54.54411.83710.03993.704-1.39523.4405-0.015-0.4558-0.11190.3329-0.08880.0238-0.1224-0.35450.05370.32770.0579-0.03330.4618-0.08680.312827.458343.810354.6276
63.441-0.1710.78822.4308-0.45444.04740.02830.2157-0.46380.16350.0738-0.24480.0844-0.2071-0.18240.2018-0.0065-0.08880.2275-0.08670.304338.050234.843153.8229
73.54430.1874-0.86865.7766-2.17655.7350.03170.2369-0.02880.1211-0.1109-0.5293-0.20610.35030.08820.3331-0.0556-0.12480.4376-0.01270.37647.345945.445652.4121
82.3203-0.2069-0.28073.7213-2.02113.2343-0.14280.1505-0.20030.3499-0.0217-0.0478-0.1765-0.02760.15570.4519-0.0502-0.13660.31590.0050.411349.991338.650368.3226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:146)A0 - 146
2X-RAY DIFFRACTION2chain 'A' and (resseq 147:290)A147 - 290
3X-RAY DIFFRACTION3chain 'B' and (resseq 0:39)B0 - 39
4X-RAY DIFFRACTION4chain 'B' and (resseq 40:62)B40 - 62
5X-RAY DIFFRACTION5chain 'B' and (resseq 63:125)B63 - 125
6X-RAY DIFFRACTION6chain 'B' and (resseq 126:179)B126 - 179
7X-RAY DIFFRACTION7chain 'B' and (resseq 180:198)B180 - 198
8X-RAY DIFFRACTION8chain 'B' and (resseq 199:290)B199 - 290

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