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- PDB-3m9u: Crystal structure of geranylgeranyl pyrophosphate synthase from l... -

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Basic information

Entry
Database: PDB / ID: 3m9u
TitleCrystal structure of geranylgeranyl pyrophosphate synthase from lactobacillus brevis atcc 367
ComponentsFarnesyl-diphosphate synthase
KeywordsTRANSFERASE / ISOPRENYL DIPHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Isoprene biosynthesis / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


(2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / cytoplasm
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
Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsPatskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York Structural GenomiX Research Consortium (NYSGXRC) / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Geranylgeranyl Pyrophosphate Synthase from Lactobacillus Brevis Atcc 367
Authors: Patskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Farnesyl-diphosphate synthase
B: Farnesyl-diphosphate synthase
C: Farnesyl-diphosphate synthase
D: Farnesyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,39326
Polymers133,3674
Non-polymers2,02622
Water12,755708
1
D: Farnesyl-diphosphate synthase
hetero molecules

A: Farnesyl-diphosphate synthase
B: Farnesyl-diphosphate synthase
C: Farnesyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,39326
Polymers133,3674
Non-polymers2,02622
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_556x,y,z+11
identity operation1_555x,y,z1
Buried area14480 Å2
ΔGint-90 kcal/mol
Surface area43020 Å2
MethodPISA
2
A: Farnesyl-diphosphate synthase
B: Farnesyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,42010
Polymers66,6842
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-36 kcal/mol
Surface area22380 Å2
MethodPISA
3
B: Farnesyl-diphosphate synthase
C: Farnesyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,42010
Polymers66,6842
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-20 kcal/mol
Surface area24270 Å2
MethodPISA
4
D: Farnesyl-diphosphate synthase
hetero molecules

C: Farnesyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,97316
Polymers66,6842
Non-polymers1,28914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area7300 Å2
ΔGint-42 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.496, 51.096, 125.928
Angle α, β, γ (deg.)95.47, 91.28, 105.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Farnesyl-diphosphate synthase


Mass: 33341.824 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / JCM 1170 / Gene: LVIS_0975 / Production host: Escherichia coli (E. coli)
References: UniProt: Q03RR4, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M SODIUM ACETATE, PH 4.5, 25% PEG3350, 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: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.77→40 Å / Num. obs: 113051 / % possible obs: 95.6 % / Observed criterion σ(I): -5 / Redundancy: 1.3 % / Biso Wilson estimate: 22.701 Å2 / Rsym value: 0.087 / Net I/σ(I): 3.4
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.3 / % possible all: 93.8

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.431 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19626 3281 3 %RANDOM
Rwork0.15819 ---
obs0.15933 106534 97.21 %-
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: 30.661 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å21.18 Å2-0.46 Å2
2---0.65 Å2-0.03 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.77→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8764 0 132 708 9604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229075
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.371.97312364
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07951177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54724.842380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.494151424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1691540
X-RAY DIFFRACTIONr_chiral_restr0.090.21434
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216808
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_it3.30325754
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.69239184
X-RAY DIFFRACTIONr_scbond_it5.80933321
X-RAY DIFFRACTIONr_scangle_it8.53353160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.769→1.815 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 228 -
Rwork0.268 7474 -
obs--93.08 %

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