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- PDB-3qqv: Crystal structure of geranylgeranyl pyrophosphate synthase from c... -

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Basic information

Entry
Database: PDB / ID: 3qqv
TitleCrystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium glutamicum complexed with isoprenyl diphosphate and magnesium
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / GERANYLGERANYL PYROPHOSPHATE SYNTHASE / ISOPRENE BIOSYNTHESIS / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / ENZYME FUNCTION INITIATIVE / EFI / PSI-2
Function / homology
Function and homology information


dimethylallyltranstransferase / isoprenoid biosynthetic process / dimethylallyltranstransferase activity / metal ion binding
Similarity search - Function
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
DIMETHYLALLYL DIPHOSPHATE / Unknown ligand / Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPatskovsky, Y. / Toro, R. / Sauder, J.M. / Poulter, C.D. / Gerlt, J.A. / Burley, S.K. / Almo, S.C. / Enzyme Function Initiative (EFI) / 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
DepositionFeb 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 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 1.6Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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_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.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.pdbx_leaving_atom_flag / _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 1.9Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1127
Polymers41,4791
Non-polymers6336
Water2,630146
1
A: Geranylgeranyl pyrophosphate synthase
hetero molecules

A: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,22314
Polymers82,9572
Non-polymers1,26612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8820 Å2
ΔGint-81 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.636, 123.636, 51.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Geranylgeranyl pyrophosphate synthase


Mass: 41478.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 / Gene: Cgl2172 / Plasmid: BC-PSGX3(BC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q8NNM1, dimethylallyltranstransferase

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Non-polymers , 5 types, 152 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15M POTASSIUM BROMIDE, PH 7.5, 30% PEG MME2000, 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: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 30934 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 12 % / Biso Wilson estimate: 41.976 Å2 / Rsym value: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
RESOLVEmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.319 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25213 975 3.2 %RANDOM
Rwork0.20782 ---
obs0.20911 29837 99.71 %-
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: 59.987 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å21.08 Å20 Å2
2--2.16 Å20 Å2
3----3.25 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 48 146 2904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212829
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9723847
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5255367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19723.731134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71115465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9791528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212163
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_it2.89421795
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.55732869
X-RAY DIFFRACTIONr_scbond_it6.34441034
X-RAY DIFFRACTIONr_scangle_it9.6097973
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 69 -
Rwork0.354 2159 -
obs--99.38 %

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