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- PDB-2vg0: Rv1086 citronellyl pyrophosphate complex -

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Basic information

Entry
Database: PDB / ID: 2vg0
TitleRv1086 citronellyl pyrophosphate complex
ComponentsSHORT-CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHETASE
KeywordsTRANSFERASE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL BIOGENESIS/DEGRADATION / SECRETED / CELL SHAPE / PRENYLTRANSFERASE
Function / homology
Function and homology information


(2Z,6E)-farnesyl diphosphate synthase / plastid membrane organization / dehydrodolichyl diphosphate synthase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / response to cold / manganese ion binding / magnesium ion binding ...(2Z,6E)-farnesyl diphosphate synthase / plastid membrane organization / dehydrodolichyl diphosphate synthase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / response to cold / manganese ion binding / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GERANYL DIPHOSPHATE / (2Z,6E)-farnesyl diphosphate synthase / (2Z,6E)-farnesyl diphosphate synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsNaismith, J.H. / Wang, W. / Dong, C.
CitationJournal: J. Mol. Biol. / Year: 2008
Title: The structural basis of chain length control in Rv1086.
Authors: Wang, W. / Dong, C. / McNeil, M. / Kaur, D. / Mahapatra, S. / Crick, D.C. / Naismith, J.H.
History
DepositionNov 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2017Group: Source and taxonomy / Structure summary / Category: entity_src_gen / struct
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _struct.title
Revision 1.4Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHORT-CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHETASE
B: SHORT-CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4197
Polymers50,5152
Non-polymers9055
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-28.4 kcal/mol
Surface area23290 Å2
MethodPQS
Unit cell
Length a, b, c (Å)58.517, 73.541, 102.561
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 SHORT-CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHETASE / RV1086 / Z-FPP SYNTHETASE / Z-ISOPRENYL DIPHOSPHATE SYNTHASE / Z-FPPS


Mass: 25257.324 Da / Num. of mol.: 2 / Fragment: RESIDUES 30-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: O53434, UniProt: P9WFF5*PLUS, (2Z,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 1.92 Å3/Da / Density % sol: 43.67 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→27 Å / Num. obs: 46922 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 25
Reflection shellResolution: 1.8→1.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALAdata reduction
MOSFLMdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→26.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.391 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2505 5.1 %RANDOM
Rwork0.173 ---
obs0.176 46921 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 56 483 4095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213683
X-RAY DIFFRACTIONr_bond_other_d0.0040.022474
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9595007
X-RAY DIFFRACTIONr_angle_other_deg0.8573.0015922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9295452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23322.778180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79515572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7521540
X-RAY DIFFRACTIONr_chiral_restr0.0720.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
X-RAY DIFFRACTIONr_nbd_refined0.2170.2913
X-RAY DIFFRACTIONr_nbd_other0.2070.22978
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21866
X-RAY DIFFRACTIONr_nbtor_other0.0860.21986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3610.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3561.52911
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57623598
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.43531661
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6144.51409
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 197
Rwork0.162 3414
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)
10.9570.0394-0.44620.73430.09550.86050.01750.0188-0.10990.115-0.0168-0.05680.04630.0254-0.0007-0.10740.0073-0.0158-0.16030.0259-0.170831.3750.111-3.065
21.0735-0.0840.24190.3390.12710.9189-0.0138-0.05880.02-0.0364-0.0123-0.01330.0171-0.03170.0261-0.1017-0.00230.02-0.1707-0.0103-0.17327.361-1.003-31.923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 256
2X-RAY DIFFRACTION2B30 - 256

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