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- PDB-3q79: Cryptococcus neoformans protein farnesyltransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3q79
TitleCryptococcus neoformans protein farnesyltransferase in complex with farnesyl-DDPTASACNIQ product
Components
  • (Farnesyltransferase ...) x 2
  • isoprenylated product
KeywordsTRANSFERASE / protein prenyltransferase
Function / homology
Function and homology information


protein prenyltransferase activity / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / zinc ion binding
Similarity search - Function
Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-3CX / FARNESYL / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å
AuthorsHast, M.A. / Beese, L.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structures of Cryptococcus neoformans Protein Farnesyltransferase Reveal Strategies for Developing Inhibitors That Target Fungal Pathogens.
Authors: Hast, M.A. / Nichols, C.B. / Armstrong, S.M. / Kelly, S.M. / Hellinga, H.W. / Alspaugh, J.A. / Beese, L.S.
History
DepositionJan 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999There is no UniPort database reference sequence available at the time of the deposition. The ...There is no UniPort database reference sequence available at the time of the deposition. The sequences presented here are of farnesyltransferase alpha subunit(residues 15-349) and beta subunit from Cryptococcus neoformans var. grubii strain H99. The first 14 residues in the alpha subunit(chain A) represent expression tag.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Farnesyltransferase alpha subunit
B: Farnesyltransferase beta subunit
P: isoprenylated product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9349
Polymers98,8543
Non-polymers1,0806
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-96 kcal/mol
Surface area30770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.900, 141.900, 130.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2228-

HOH

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Components

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Farnesyltransferase ... , 2 types, 2 molecules AB

#1: Protein Farnesyltransferase alpha subunit


Mass: 40913.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Strain: H99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55S71*PLUS
#2: Protein Farnesyltransferase beta subunit


Mass: 56806.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Strain: H99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55QV6*PLUS

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide isoprenylated product


Mass: 1134.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic substrate

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Non-polymers , 5 types, 389 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-3CX / (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO4S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 15% PEG 4K, 100mM CAPSO pH 9.5, 100mM NaCl, 150mM Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 44750 / % possible obs: 96.3 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.6 Å / % possible all: 66.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX1.6.1_336refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.506→47.954 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 2239 5 %
Rwork0.2118 --
obs0.2141 44748 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.64 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.5255 Å20 Å2-0 Å2
2--6.5255 Å20 Å2
3----13.0511 Å2
Refinement stepCycle: LAST / Resolution: 2.506→47.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6370 0 66 383 6819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046626
X-RAY DIFFRACTIONf_angle_d0.7379004
X-RAY DIFFRACTIONf_dihedral_angle_d14.2962463
X-RAY DIFFRACTIONf_chiral_restr0.046958
X-RAY DIFFRACTIONf_plane_restr0.0051159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5061-2.59560.34842000.26943785X-RAY DIFFRACTION88
2.5956-2.69960.38122160.28154104X-RAY DIFFRACTION95
2.6996-2.82240.29362260.21394300X-RAY DIFFRACTION100
2.8224-2.97120.25112280.19384328X-RAY DIFFRACTION100
2.9712-3.15730.25622300.19674358X-RAY DIFFRACTION100
3.1573-3.4010.25352270.21954321X-RAY DIFFRACTION99
3.401-3.74320.30212100.27013995X-RAY DIFFRACTION91
3.7432-4.28450.27442230.20344220X-RAY DIFFRACTION96
4.2845-5.39690.17382330.14154442X-RAY DIFFRACTION100
5.3969-47.96240.17972460.1654656X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.3434 Å / Origin y: -31.4456 Å / Origin z: -2.6667 Å
111213212223313233
T0.0539 Å2-0.0511 Å2-0.0089 Å2-0.0213 Å2-0.013 Å2--0.0363 Å2
L0.0671 °20.0022 °2-0.0046 °2-0.0403 °2-0.0965 °2--0.235 °2
S0 Å °-0.0067 Å °-0.0105 Å °-0.0198 Å °0.0007 Å °-0.0014 Å °0.0088 Å °0.0056 Å °-0.0037 Å °
Refinement TLS groupSelection details: all

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