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- PDB-4jyx: Crystal structure of polyprenyl synthase PATL_3739 (TARGET EFI-50... -

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Basic information

Entry
Database: PDB / ID: 4jyx
TitleCrystal structure of polyprenyl synthase PATL_3739 (TARGET EFI-509195) FROM PSEUDOALTEROMONAS ATLANTICA, COMPLEX WITH INORGANIC PHOSPHATE AND AN UNKNOWN LIGAND
ComponentsTrans-hexaprenyltranstransferaseHeptaprenyl diphosphate synthase
KeywordsTRANSFERASE / ISOPRENOID SYNTHASE / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


heptaprenyl diphosphate synthase activity => GO:0000010 / heptaprenyl diphosphate synthase / isoprenoid biosynthetic process
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
PHOSPHATE ION / Unknown ligand / Trans-hexaprenyltranstransferase
Similarity search - Component
Biological speciesPseudoalteromonas atlantica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal Structure of Isoprenoid Synthase Patl_3739 from Pseudoalteromonas Atlantica
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C.
History
DepositionApr 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 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 / 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: Trans-hexaprenyltranstransferase
B: Trans-hexaprenyltranstransferase
C: Trans-hexaprenyltranstransferase
D: Trans-hexaprenyltranstransferase
E: Trans-hexaprenyltranstransferase
F: Trans-hexaprenyltranstransferase
G: Trans-hexaprenyltranstransferase
H: Trans-hexaprenyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,61225
Polymers306,3778
Non-polymers1,23517
Water10,557586
1
B: Trans-hexaprenyltranstransferase
D: Trans-hexaprenyltranstransferase
hetero molecules

F: Trans-hexaprenyltranstransferase
G: Trans-hexaprenyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,75812
Polymers153,1884
Non-polymers5708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area12780 Å2
ΔGint-127 kcal/mol
Surface area47700 Å2
MethodPISA
2
B: Trans-hexaprenyltranstransferase
D: Trans-hexaprenyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8796
Polymers76,5942
Non-polymers2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-51 kcal/mol
Surface area25350 Å2
MethodPISA
3
E: Trans-hexaprenyltranstransferase
H: Trans-hexaprenyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8796
Polymers76,5942
Non-polymers2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-54 kcal/mol
Surface area25520 Å2
MethodPISA
4
F: Trans-hexaprenyltranstransferase
G: Trans-hexaprenyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8796
Polymers76,5942
Non-polymers2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-54 kcal/mol
Surface area25540 Å2
MethodPISA
5
A: Trans-hexaprenyltranstransferase
C: Trans-hexaprenyltranstransferase
hetero molecules

E: Trans-hexaprenyltranstransferase
H: Trans-hexaprenyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,85313
Polymers153,1884
Non-polymers6659
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area12980 Å2
ΔGint-133 kcal/mol
Surface area47770 Å2
MethodPISA
6
A: Trans-hexaprenyltranstransferase
C: Trans-hexaprenyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9747
Polymers76,5942
Non-polymers3805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-57 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.104, 152.907, 284.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Trans-hexaprenyltranstransferase / Heptaprenyl diphosphate synthase


Mass: 38297.117 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas atlantica (bacteria) / Strain: T6c / ATCC BAA-1087 / Gene: Patl_3739 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q15PE7, heptaprenyl diphosphate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.6 Å3/Da / Density % sol: 52.81 %
Crystal growpH: 4.2
Details: 0.2M LITHIUM SULFATE, 0.1M SODIUM HYDROGEN PHOSPHATE:CITRIC ACID, PH 4.2, 20% PEG1000, VAPOR DIFFUSIO SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2013 / Details: MIRRORS
RadiationMonochromator: Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 141635 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 8 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 4.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JXY

4jxy


Resolution: 2.3→48.4 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.377 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23882 4257 3 %RANDOM
Rwork0.17714 ---
obs0.17896 137269 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.434 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å20 Å20 Å2
2---1.27 Å2-0 Å2
3---4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19424 0 97 586 20107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01919825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219039
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.97126920
X-RAY DIFFRACTIONr_angle_other_deg0.691343715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.34552510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23826.068918
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.981153502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1921577
X-RAY DIFFRACTIONr_chiral_restr0.0460.23223
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0222591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024226
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 296 -
Rwork0.282 9490 -
obs--94.15 %

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