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- PDB-2vg3: Rv2361 with citronellyl pyrophosphate -

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Basic information

Entry
Database: PDB / ID: 2vg3
TitleRv2361 with citronellyl pyrophosphate
ComponentsUNDECAPRENYL PYROPHOSPHATE SYNTHETASE
KeywordsTRANSFERASE / CELL WALL BIOGENESIS/DEGRADATION / CELL CYCLE / PRENYL TRANSFERASE / PEPTIDOGLYCAN SYNTHESIS
Function / homology
Function and homology information


trans,polycis-decaprenyl diphosphate synthase / all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / Z-farnesyl diphosphate synthase activity / dehydrodolichyl diphosphate synthase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / polyprenol biosynthetic process / prenyltransferase activity / manganese ion binding / magnesium ion binding ...trans,polycis-decaprenyl diphosphate synthase / all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / Z-farnesyl diphosphate synthase activity / dehydrodolichyl diphosphate synthase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / polyprenol biosynthetic process / prenyltransferase activity / 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 / PHOSPHATE ION / Decaprenyl diphosphate synthase / Decaprenyl diphosphate synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Sep 28, 2011Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.3Feb 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 1.4May 2, 2018Group: Data collection / Category: diffrn_detector / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
B: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
C: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
D: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,74119
Polymers129,8434
Non-polymers1,89815
Water7,692427
1
A: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
C: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8829
Polymers64,9222
Non-polymers9607
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-53.7 kcal/mol
Surface area23580 Å2
MethodPISA
2
B: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
D: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,85910
Polymers64,9222
Non-polymers9388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-46.5 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.870, 86.870, 184.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
UNDECAPRENYL PYROPHOSPHATE SYNTHETASE / UPP SYNTHETASE / UNDECAPRENYL DIPHOSPHATE SYNTHASE / DI-TRANS POLY-CIS-DECAPRENYLCISTRANSFERASE / UDS / RV2361


Mass: 32460.809 Da / Num. of mol.: 4 / Fragment: RESIDUES 13-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60479, UniProt: P9WFF7*PLUS, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]

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Non-polymers , 7 types, 442 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20O7P2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.86 Å3/Da / Density % sol: 60.14 %
Description: NOTE TWO DATA SETS, ONE WITH TWINNED DATA AND ONE WITH DETWINNED DATA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Type: ESRF / Wavelength: 0.9762
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→5 Å / Num. obs: 134070 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→75.16 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.453 / SU ML: 0.083 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS TWINNED DATA BOTH THE TWINNED AND THE DETWINNED DATA USED IN REFINEMENT HAVE BEEN DEPOSITED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 6594 5 %RANDOM
Rwork0.203 ---
obs0.204 125242 91.6 %-
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: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→75.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9141 0 108 427 9676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229535
X-RAY DIFFRACTIONr_bond_other_d0.0020.026768
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.95912953
X-RAY DIFFRACTIONr_angle_other_deg0.8843.00116145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39751141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91121.851470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.129151515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8115128
X-RAY DIFFRACTIONr_chiral_restr0.0690.21361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022112
X-RAY DIFFRACTIONr_nbd_refined0.2130.21988
X-RAY DIFFRACTIONr_nbd_other0.2030.27461
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24677
X-RAY DIFFRACTIONr_nbtor_other0.0830.24943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2392
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7521.57442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87729254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.59534506
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1914.53694
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 473
Rwork0.248 8563
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)
10.6851-0.0236-0.00230.9433-0.09681.72-0.0325-0.0781-0.03880.04230.01540.02350.02960.01010.0172-0.1330.05770.0065-0.15270.0129-0.12513.808229.3957451.9432
21.3374-0.2923-0.18861.14640.00911.44540.08540.05910.0368-0.1183-0.0533-0.0644-0.06690.0275-0.0321-0.07120.06080.03-0.16460.0095-0.10236.9744-7.3126446.2911
30.66740.19210.19071.6181-0.03441.0541-0.00940.05070.083-0.069-0.0387-0.276-0.12160.24410.0482-0.07940.00790.0282-0.0620.0223-0.064329.172751.3398431.1617
41.5807-0.2088-0.00511.3672-0.24091.36590.0614-0.0609-0.0367-0.00570.04280.2223-0.0191-0.1926-0.1042-0.08230.04430.0077-0.07380.0556-0.06489.7148-9.8502466.154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 296
2X-RAY DIFFRACTION2B13 - 296
3X-RAY DIFFRACTION3C13 - 296
4X-RAY DIFFRACTION4D14 - 296

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