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- PDB-2vg2: Rv2361 with IPP -

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Basic information

Entry
Database: PDB / ID: 2vg2
TitleRv2361 with IPP
ComponentsUNDECAPRENYL PYROPHOSPHATE SYNTHETASE
KeywordsTRANSFERASE / CELL WALL BIOGENESIS/DEGRADATION / CELL CYCLE / CELL SHAPE / CELL DIVISION / 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 / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / prenyltransferase activity / manganese ion binding / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHATE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / PHOSPHATE ION / Decaprenyl diphosphate synthase / Decaprenyl diphosphate synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 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 1.3May 2, 2018Group: Data collection / Category: diffrn_detector / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4May 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: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
B: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
C: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
D: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,47327
Polymers129,8434
Non-polymers2,62923
Water13,601755
1
A: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
C: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,57317
Polymers64,9222
Non-polymers1,65115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-15.1 kcal/mol
Surface area28890 Å2
MethodPQS
2
B: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
D: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,90010
Polymers64,9222
Non-polymers9788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-20.8 kcal/mol
Surface area28700 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.074, 87.074, 183.711
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 , 6 types, 778 molecules

#2: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O7P2
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 56.61 % / Description: NONE

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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: 1.95→75 Å / Num. obs: 111969 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.8 / % possible all: 95

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→69.84 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.525 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 5589 5 %RANDOM
Rwork0.185 ---
obs0.187 106312 98.5 %-
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: 33.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.95→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9128 0 153 755 10036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229525
X-RAY DIFFRACTIONr_bond_other_d0.0020.026793
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.96212956
X-RAY DIFFRACTIONr_angle_other_deg0.868316240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82351137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.921.816468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.075151512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.86515128
X-RAY DIFFRACTIONr_chiral_restr0.0680.21356
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022109
X-RAY DIFFRACTIONr_nbd_refined0.210.22101
X-RAY DIFFRACTIONr_nbd_other0.2070.27666
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24657
X-RAY DIFFRACTIONr_nbtor_other0.0810.24915
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2608
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7221.57401
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82629228
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.50334528
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1674.53724
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 390
Rwork0.229 7599
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)
10.9979-0.1014-0.13690.8191-0.03462.8847-0.00470.0421-0.0192-0.1345-0.0418-0.04750.12640.05930.0466-0.16830.06530.0138-0.3155-0.0113-0.215511.19827.966-3.105
21.2785-0.1676-0.13212.0477-0.34322.2514-0.1218-0.0941-0.07660.30120.19060.0789-0.0896-0.1312-0.0688-0.13240.15020.0378-0.21530.0436-0.191731.071-10.7772.578
32.268-0.3454-0.16551.05940.3821.6336-0.02290.0911-0.29420.0253-0.03610.2820.201-0.43110.059-0.1676-0.02350.0183-0.14480.0077-0.1328-15.53225.16117.658
41.92310.1505-0.71642.4189-0.17512.42610.1494-0.09070.32780.12510.1241-0.2237-0.52210.1334-0.2735-0.020.01310.0849-0.2122-0.0585-0.12247.27711.486-17.202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 296
2X-RAY DIFFRACTION2B13 - 295
3X-RAY DIFFRACTION3C13 - 296
4X-RAY DIFFRACTION4D14 - 296

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