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- PDB-6c56: Crystal structure of mutant human geranylgeranyl pyrophosphate sy... -

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Basic information

Entry
Database: PDB / ID: 6c56
TitleCrystal structure of mutant human geranylgeranyl pyrophosphate synthase (Y246D) in its Apo form
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / ISOPRENOID PATHWAY / ISOPENTENYL TRANSFERASE
Function / homology
Function and homology information


isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / Cholesterol biosynthesis ...isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / Cholesterol biosynthesis / geranyltranstransferase activity / farnesyltranstransferase activity / prenyltransferase activity / isoprenoid biosynthetic process / Activation of gene expression by SREBF (SREBP) / Z disc / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / 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
Chem-VT0 / Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPark, J. / Ta, V. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Unraveling the Prenylation-Cancer Paradox in Multiple Myeloma with Novel Geranylgeranyl Pyrophosphate Synthase (GGPPS) Inhibitors.
Authors: Lacbay, C.M. / Waller, D.D. / Park, J. / Gomez Palou, M. / Vincent, F. / Huang, X.F. / Ta, V. / Berghuis, A.M. / Sebag, M. / Tsantrizos, Y.S.
History
DepositionJan 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2543
Polymers74,8532
Non-polymers4011
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.100, 185.100, 115.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-401-

VT0

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Farnesyltranstransferase / Geranylgeranyl diphosphate synthase / Geranyltranstransferase


Mass: 37426.488 Da / Num. of mol.: 2 / Mutation: Y246D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGPS1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95749, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-VT0 / {[(2-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)


Mass: 401.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3O6P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.26 M ammonium phosphate, 35% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→54.39 Å / Num. obs: 24791 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.014 / Net I/σ(I): 36.5
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 10 % / Rmerge(I) obs: 1.129 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1791 / Rpim(I) all: 0.397 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q80

2q80


Resolution: 2.8→54.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 27.312 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.452 / ESU R Free: 0.293 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1270 5.1 %RANDOM
Rwork0.18522 ---
obs0.18804 23520 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 100.055 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å20 Å2
2---1.88 Å20 Å2
3---3.76 Å2
Refinement stepCycle: 1 / Resolution: 2.8→54.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 25 39 4380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194438
X-RAY DIFFRACTIONr_bond_other_d0.0030.023952
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.9726040
X-RAY DIFFRACTIONr_angle_other_deg1.2053.0019128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0425546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92924.804204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88215706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9931516
X-RAY DIFFRACTIONr_chiral_restr0.1120.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02898
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3536.1912205
X-RAY DIFFRACTIONr_mcbond_other3.3516.1912204
X-RAY DIFFRACTIONr_mcangle_it4.9039.2872744
X-RAY DIFFRACTIONr_mcangle_other4.9029.2882745
X-RAY DIFFRACTIONr_scbond_it4.0896.4152233
X-RAY DIFFRACTIONr_scbond_other4.0886.4162234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0259.5223297
X-RAY DIFFRACTIONr_long_range_B_refined7.72673.6495119
X-RAY DIFFRACTIONr_long_range_B_other7.72573.6475120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.803→2.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 84 -
Rwork0.307 1701 -
obs--99.66 %
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)
13.71390.1597-1.78422.0582-0.06526.27140.0123-0.4558-0.90980.5504-0.15180.04380.33460.5170.13950.31790.0469-0.00060.13580.04190.3282-37.559410.3077-39.8976
24.19740.965-0.5062.6797-1.15262.2205-0.0658-0.744-0.85490.7026-0.4314-0.52620.14730.70960.49720.5090.1106-0.15280.370.18660.3918-20.942921.2741-35.1993
32.92830.1904-2.25772.80890.22092.4770.04670.33510.10070.3114-0.24860.8818-0.1175-0.51490.20180.18170.1070.04830.2033-0.14110.3202-50.570926.0403-48.355
44.0930.90460.13084.4211.2323.7970.21351.18060.5245-0.8173-0.18880.7916-0.7888-0.7873-0.02480.38070.1989-0.12250.7806-0.06830.7091-64.507221.1488-63.3686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 106
2X-RAY DIFFRACTION2A107 - 295
3X-RAY DIFFRACTION3B0 - 171
4X-RAY DIFFRACTION4B172 - 295

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