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- PDB-3lk5: Crystal structure of putative Geranylgeranyl pyrophosphate syntha... -

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Basic information

Entry
Database: PDB / ID: 3lk5
TitleCrystal structure of putative Geranylgeranyl pyrophosphate synthase from Corynebacterium glutamicum
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / Geranylgeranyl pyrophosphate synthase / Isoprene biosynthesis / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


dimethylallyltranstransferase / dimethylallyltranstransferase activity / isoprenoid biosynthetic process
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
Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Toro, R. / Patskovsky, Y. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative Geranylgeranyl pyrophosphate synthase from Corynebacterium glutamicum Atcc 13032
Authors: Malashkevich, V.N. / Toro, R. / Patskovsky, Y. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5712
Polymers41,4791
Non-polymers921
Water3,495194
1
A: Geranylgeranyl pyrophosphate synthase
hetero molecules

A: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1424
Polymers82,9572
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-1/31
Buried area4550 Å2
ΔGint-36 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.434, 125.434, 52.067
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG4000, 0.2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 37221 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Χ2: 0.983 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.609 / Num. unique all: 4613 / Χ2: 0.81 / % possible all: 95.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.7 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.115 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1870 5 %RANDOM
Rwork0.168 ---
obs0.17 37221 99.75 %-
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 max: 89.93 Å2 / Biso mean: 34.455 Å2 / Biso min: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 6 194 2723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212586
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9653510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9565337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36424.083120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62715430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9751522
X-RAY DIFFRACTIONr_chiral_restr0.0970.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211962
X-RAY DIFFRACTIONr_mcbond_it1.2733.51657
X-RAY DIFFRACTIONr_mcangle_it4.216502643
X-RAY DIFFRACTIONr_scbond_it9.22350929
X-RAY DIFFRACTIONr_scangle_it1.7434.5864
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 131 -
Rwork0.207 2566 -
all-2697 -
obs--99.7 %
Refinement TLS params.Method: refined / Origin x: -1.4547 Å / Origin y: 94.4191 Å / Origin z: 1.0118 Å
111213212223313233
T0.0717 Å20.0069 Å2-0.0016 Å2-0.0339 Å20.0248 Å2--0.0221 Å2
L0.2987 °20.5006 °2-0.2764 °2-1.4213 °2-0.3503 °2--0.5109 °2
S-0.0496 Å °0.0492 Å °0.0207 Å °0.0527 Å °0.1305 Å °0.0393 Å °0.0254 Å °-0.1011 Å °-0.0809 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 370
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A381 - 575

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