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- PDB-4kkm: Crystal structure of a FPP/GFPP synthase (Target EFI-501952) from... -

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Entry
Database: PDB / ID: 4kkm
TitleCrystal structure of a FPP/GFPP synthase (Target EFI-501952) from Zymomonas mobilis, apo structure
ComponentsPolyprenyl synthetase
KeywordsTRANSFERASE / isoprenoid synthase / FPP GGPP synthase / Enzyme Function Initiative / structural genomics
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
: / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / 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
ACETATE ION / Geranyltranstransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: To be Published
Title: Crystal structure of a FPP/GFPP synthase (Target EFI-501952) from Zymomonas mobilis, apo structure
Authors: 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. ...Authors: 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)
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: Polyprenyl synthetase
B: Polyprenyl synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9755
Polymers69,7842
Non-polymers1913
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-50 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.414, 73.414, 229.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Polyprenyl synthetase / isoprenoid synthase


Mass: 34891.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria)
Strain: ATCC 31821 / ZM4 / Gene: ZMO0855 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5NP81, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM magnesium chloride), reservoir (0.2 M calcium acetate, 0.1 M MES, pH 6.0, 20% PEG8000), cryoprotectant ...Details: protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM magnesium chloride), reservoir (0.2 M calcium acetate, 0.1 M MES, pH 6.0, 20% PEG8000), cryoprotectant (reservoir + 20% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Jul 20, 2012 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→69.921 Å / Num. all: 50674 / Num. obs: 50674 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.138 / Rsym value: 0.138 / Net I/σ(I): 14.2
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-214.50.610551572801.193100
2-2.1214.51.19922768360.69100
2.12-2.2714.41.89385164950.418100
2.27-2.4514.52.98786660700.265100
2.45-2.6914.44.48033255610.173100
2.69-314.46.17357351010.12100
3-3.4714.25.66448545470.112100
3.47-4.2513.565234738640.101100
4.25-6.0113.86.94250730910.077100
6.01-34.96112.416.82269718290.03399.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M0G

3m0g


Resolution: 1.9→34.961 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8685 / SU ML: 0.21 / σ(F): 0 / σ(I): 0 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 2572 5.09 %RANDOM
Rwork0.181 ---
all0.1823 50565 --
obs0.1823 50565 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.75 Å2 / Biso mean: 43.8285 Å2 / Biso min: 17.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 11 330 4558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054352
X-RAY DIFFRACTIONf_angle_d0.8865885
X-RAY DIFFRACTIONf_chiral_restr0.055689
X-RAY DIFFRACTIONf_plane_restr0.005774
X-RAY DIFFRACTIONf_dihedral_angle_d13.4081626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.93660.34771410.273426392780
1.9366-1.97610.27071600.235826012761
1.9761-2.01910.26141340.223425872721
2.0191-2.0660.24881580.208825982756
2.066-2.11770.22531420.189226322774
2.1177-2.17490.22461460.178226232769
2.1749-2.23890.22211460.181326052751
2.2389-2.31120.19591390.177926632802
2.3112-2.39380.22431200.174826362756
2.3938-2.48960.22091340.172526512785
2.4896-2.60280.20741420.172526482790
2.6028-2.740.23491470.178426712818
2.74-2.91160.22631350.178426532788
2.9116-3.13630.22391680.189426532821
3.1363-3.45170.211560.182626792835
3.4517-3.95050.18151270.164427332860
3.9505-4.9750.1451310.153327842915
4.975-34.96650.18991460.197129373083
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)
11.80161.77671.00962.64620.54870.7522-0.09170.226-0.89080.0565-0.04360.77640.6099-0.6510.75990.1845-0.28630.4750.6195-0.39761.35835.666931.640295.3936
20.3824-0.07120.26033.1531-0.40580.2544-0.06430.0985-0.0366-0.043-0.29140.9578-0.2979-0.52860.21060.26980.0922-0.0480.4075-0.1420.46937.845754.506495.7068
30.76310.8689-0.32922.7977-0.20371.3303-0.03690.0521-0.24120.1572-0.45171.04360.4903-0.49070.18060.3831-0.11350.21090.3204-0.14180.590814.922835.173296.4527
40.0494-0.11530.13831.81281.45662.59020.3060.9943-0.6117-0.7153-0.48520.35280.1823-0.03410.09330.48130.093-0.13070.588-0.15460.46215.393550.022880.7247
52.4498-0.4621-0.13722.3931.03612.0611-0.1604-0.0541-0.37470.706-0.17240.35820.468-0.18180.16130.4158-0.02080.12990.2082-0.03430.305520.885842.1537103.6539
61.18690.0696-0.91850.49550.24870.8436-0.19160.1929-0.1364-0.14620.1229-0.03080.01360.02830.02670.2698-0.03120.03760.246-0.03710.293133.572438.156783.4798
71.4502-0.31030.4130.1132-0.15180.23180.2014-0.1525-0.10741.1589-0.14580.94420.1721-0.1389-0.26340.7504-0.08140.19620.2122-0.01570.400523.391728.6416101.0544
82.1548-0.23830.64091.6481-0.12183.7263-0.03920.0334-0.17570.5070.05040.18110.35020.11920.0820.5145-0.02290.04060.2542-0.03680.316525.690925.100988.8692
92.16480.5199-0.97590.487-0.0393.0161-0.27260.395-0.23760.37470.2370.11610.3136-0.0692-0.07530.522-0.06250.0810.2711-0.07280.361327.086322.500179.5344
103.04440.2206-2.37420.1372-0.53523.03550.30740.2033-0.13270.8474-0.03990.60040.4561-0.7011-0.37750.8184-0.27660.22160.4518-0.13360.7215.715618.297392.4291
111.7115-0.3039-0.95712.60541.90233.3219-0.1385-0.12880.1665-0.11640.3688-0.2713-0.29580.4912-0.09310.2242-0.01030.00740.2835-0.03980.271836.203555.6593100.714
120.999-0.69170.00721.44310.84272.3979-0.1224-0.08170.08720.18190.07210.0635-0.23280.09040.05820.25710.0491-0.010.2163-0.03330.200423.187964.3466110.674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 23 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 42 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 87 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 108 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 150 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 185 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 203 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 228 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 229 through 278 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 279 through 295 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 128 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 129 through 294 )B0

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