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- PDB-3q2q: Crystal structure of geranylgeranyl pyrophosphate synthase from C... -

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Basic information

Entry
Database: PDB / ID: 3q2q
TitleCrystal structure of geranylgeranyl pyrophosphate synthase from Corynebacterium glutamicum complexed with calcium and isoprenyl diphosphate
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / ISOPRENYL DIPHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / ISOPRENE BIOSYNTHESIS / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


heptaprenyl diphosphate synthase activity / heptaprenyl diphosphate synthase / isoprenoid biosynthetic process / metal ion binding
Similarity search - Function
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
DIMETHYLALLYL DIPHOSPHATE / Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å
AuthorsPatskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Poulter, C.D. / Gerlt, J.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
Authors: Wallrapp, F.H. / Pan, J.J. / Ramamoorthy, G. / Almonacid, D.E. / Hillerich, B.S. / Seidel, R. / Patskovsky, Y. / Babbitt, P.C. / Almo, S.C. / Jacobson, M.P. / Poulter, C.D.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2013Group: Database references
Revision 1.3Mar 27, 2013Group: Database references
Revision 1.4Apr 24, 2013Group: Database references
Revision 1.5May 8, 2013Group: Non-polymer description
Revision 1.6May 14, 2014Group: Data collection
Revision 1.7Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.8Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_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_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
Revision 1.9Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6297
Polymers39,0791
Non-polymers5516
Water3,675204
1
A: Geranylgeranyl pyrophosphate synthase
hetero molecules

A: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,25914
Polymers78,1582
Non-polymers1,10112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area5710 Å2
ΔGint-83 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.659, 71.659, 150.919
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase / PUTATIVE OCTAPRENYL-DIPHOSPHATE SYNTHASE PROTEIN


Mass: 39078.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg0559, Cgl0473, ispB / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NT37, heptaprenyl diphosphate synthase, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 57.09 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M SODIUM ACETATE, PH 4.5, 30% PEG400, 200MM CALCIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 36231 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 6.4 % / Biso Wilson estimate: 37.374 Å2 / Rsym value: 0.075 / Net I/σ(I): 10.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 3LMD

3lmd


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.158 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21761 1118 3.1 %RANDOM
Rwork0.18317 ---
obs0.18428 34942 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.085 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20.99 Å20 Å2
2--1.98 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 29 204 2631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222588
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.031.9763535
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9285344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56524.672122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6615430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8161517
X-RAY DIFFRACTIONr_chiral_restr0.0680.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211977
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.52121622
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.09832625
X-RAY DIFFRACTIONr_scbond_it6.9224966
X-RAY DIFFRACTIONr_scangle_it10.1966898
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 82 -
Rwork0.332 2519 -
obs--99.12 %

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