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- PDB-3npk: The crystal structure of geranyltranstransferase from Campylobact... -

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Basic information

Entry
Database: PDB / ID: 3npk
TitleThe crystal structure of geranyltranstransferase from Campylobacter jejuni
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / isoprene biosynthesis / SGX / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha / PYROPHOSPHATE / :
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of geranyltranstransferase from Campylobacter jejuni
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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
Revision 1.3Dec 27, 2023Group: 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: Geranyltranstransferase
B: Geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0235
Polymers66,5752
Non-polymers4483
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-57 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.772, 97.957, 66.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Geranyltranstransferase


Mass: 33287.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: RM1221 / Gene: CJE1816, ispA / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) Codon+ril Stratagene
References: UniProt: Q5HSE9, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 97745 / % possible obs: 94.75 % / Redundancy: 13.7 % / Biso Wilson estimate: 14.22 Å2 / Rmerge(I) obs: 0.176 / Net I/σ(I): 15.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10137 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→36.629 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 15.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1851 4877 4.99 %
Rwork0.1564 --
obs0.1578 97745 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.616 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5196 Å20 Å20 Å2
2---0.0657 Å2-0 Å2
3---0.5853 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4171 0 24 497 4692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084275
X-RAY DIFFRACTIONf_angle_d1.115774
X-RAY DIFFRACTIONf_dihedral_angle_d17.8031596
X-RAY DIFFRACTIONf_chiral_restr0.072680
X-RAY DIFFRACTIONf_plane_restr0.004735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.51720.22841510.18112662X-RAY DIFFRACTION83
1.5172-1.53510.23181490.17892747X-RAY DIFFRACTION85
1.5351-1.55380.21411490.16042858X-RAY DIFFRACTION87
1.5538-1.57350.19291480.14672820X-RAY DIFFRACTION89
1.5735-1.59420.19761470.14352882X-RAY DIFFRACTION89
1.5942-1.6160.18761490.13612853X-RAY DIFFRACTION89
1.616-1.63910.20641440.13262942X-RAY DIFFRACTION90
1.6391-1.66360.17051570.12552938X-RAY DIFFRACTION91
1.6636-1.68960.18051680.12242945X-RAY DIFFRACTION90
1.6896-1.71730.15311530.12162987X-RAY DIFFRACTION92
1.7173-1.74690.17851450.12263024X-RAY DIFFRACTION93
1.7469-1.77870.17471470.12173036X-RAY DIFFRACTION94
1.7787-1.81290.15781790.11773035X-RAY DIFFRACTION94
1.8129-1.84990.16511910.11613085X-RAY DIFFRACTION96
1.8499-1.89010.16931490.11453110X-RAY DIFFRACTION96
1.8901-1.93410.16631520.11923093X-RAY DIFFRACTION96
1.9341-1.98240.15911840.12913154X-RAY DIFFRACTION97
1.9824-2.0360.18421820.12483202X-RAY DIFFRACTION98
2.036-2.09590.16561670.13083221X-RAY DIFFRACTION98
2.0959-2.16360.16831730.12393194X-RAY DIFFRACTION98
2.1636-2.24090.16571690.13263212X-RAY DIFFRACTION98
2.2409-2.33060.17821800.13873248X-RAY DIFFRACTION99
2.3306-2.43660.16921710.14663252X-RAY DIFFRACTION99
2.4366-2.56510.1651520.14863286X-RAY DIFFRACTION100
2.5651-2.72570.19771740.15613250X-RAY DIFFRACTION99
2.7257-2.93610.18061830.16783276X-RAY DIFFRACTION100
2.9361-3.23140.1971710.17383315X-RAY DIFFRACTION100
3.2314-3.69860.17221580.16943349X-RAY DIFFRACTION100
3.6986-4.65840.19541710.16823371X-RAY DIFFRACTION100
4.6584-36.63980.19531640.20173521X-RAY DIFFRACTION100

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