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- PDB-4kqs: Crystal Structure of Farnesyl Pyrophosphate Synthase Mutant (Y204... -

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Basic information

Entry
Database: PDB / ID: 4kqs
TitleCrystal Structure of Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / Isoprene biosynthesis / Lipid synthesis / steroid biosynthesis / dimethylallyl pyrophosphate / Isoprenoid Pathway / Cholesterol Synthesis / Bisphosphonates
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / 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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Chem-RIS / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBarnett, B.L. / Tsoumpra, M.K. / Muniz, J.R.C.
CitationJournal: To be Published
Title: Crystal Structure of Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate
Authors: Tsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Pilka, E. / Kwaasi, A. / Kavanagh, K.L. / Evdokimov, A.G. / Walter, R.L. / Ebetino, F.H. / Oppermann, U. / Russell, R.G.G. / Dunford, J.E.
History
DepositionMay 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6556
Polymers43,0531
Non-polymers6025
Water7,530418
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,31012
Polymers86,1062
Non-polymers1,20410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7010 Å2
ΔGint-81 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.590, 111.590, 66.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-576-

HOH

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Components

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase / FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / ...FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 43052.887 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 / Mutation: Y204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: PET 11 Derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate / Risedronic acid


Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NH4Cl, PEG6000, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 3, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→35.29 Å / Num. all: 30003 / Num. obs: 30003 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Biso Wilson estimate: 30.14 Å2 / Rmerge(I) obs: 0.163 / Rsym value: 0.163 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.97-2.08199.8
2.08-35.29199.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CP6

3cp6


Resolution: 1.97→31.13 Å / Cor.coef. Fo:Fc: 0.9512 / Cor.coef. Fo:Fc free: 0.9332 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 1523 5.08 %RANDOM
Rwork0.1703 ---
all0.172 30003 --
obs0.172 29970 99.65 %-
Displacement parametersBiso mean: 33.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.5665 Å20 Å20 Å2
2--2.5665 Å20 Å2
3----5.133 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.97→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 34 418 3171
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092844HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.893866HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1360SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes410HARMONIC5
X-RAY DIFFRACTIONt_it2844HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion2.76
X-RAY DIFFRACTIONt_chiral_improper_torsion361SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3873SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.04 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2529 172 5.93 %
Rwork0.2213 2728 -
all0.2232 2900 -
obs--99.65 %
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)
12.34091.89991.45293.49051.42510.2351-0.0748-0.1470.13960.09160.1362-0.0776-0.16230.306-0.06140.0218-0.0414-0.0209-0.0746-0.0515-0.026529.94110.203326.6859
20-0.5541-0.68211.58261.27782.3859-0.0328-0.21080.14420.1602-0.0021-0.0118-0.0068-0.01220.0349-0.00820.0084-0.0477-0.042-0.0007-0.039926.3074-16.532632.2101
30.5245-0.45720.49732.8860.25850.75360.0230.0408-0.03940.066-0.0799-0.0816-0.17080.02540.05690.0948-0.01870.0472-0.04410.00810.054225.70076.32816.9364
40.5701-0.2214-0.11891.4776-0.03110.5126-0.0002-0.04270.02010.10860.0072-0.0924-0.087-0.0144-0.007-0.0392-0.0158-0.0024-0.040.0138-0.027123.719-11.86117.6189
50.775-0.8037-0.241.48220.21780.63310.09260.09330.0961-0.2594-0.0461-0.1524-0.1320.0039-0.04640.0024-0.00380.0528-0.04810.03210.019530.646-10.77442.2449
62.23770.10090.01220.5148-0.45262.18960.1450.13130.0499-0.29490.1088-0.25850.080.133-0.25380.01770.02910.0949-0.0867-0.0139-0.020443.7724-23.2802-7.8651
70.00380.0440.61160.0895-0.12290.3716-0.03440.05510.0712-0.1680.1157-0.2626-0.13650.1456-0.08130.0401-0.00780.1388-0.0580.03540.07341.8101-7.9061-4.4486
800.0736-2.09572.37770.85770.01650.00360.0396-0.0033-0.026-0.0099-0.149-0.18720.11650.00630.0285-0.02210.0305-0.04170.006-0.022732.32055.15955.2863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|9 - 29}A9 - 29
2X-RAY DIFFRACTION2{A|30 - 52}A30 - 52
3X-RAY DIFFRACTION3{A|53 - 78}A53 - 78
4X-RAY DIFFRACTION4{A|79 - 176}A79 - 176
5X-RAY DIFFRACTION5{A|177 - 268}A177 - 268
6X-RAY DIFFRACTION6{A|269 - 294}A269 - 294
7X-RAY DIFFRACTION7{A|295 - 332}A295 - 332
8X-RAY DIFFRACTION8{A|333 - 353}A333 - 353

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