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- PDB-4w4r: Crystal structure of ent-kaurene synthase BJKS from bradyrhizobiu... -

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Basic information

Entry
Database: PDB / ID: 4w4r
TitleCrystal structure of ent-kaurene synthase BJKS from bradyrhizobium japonicum
ComponentsUncharacterized protein blr2150
KeywordsBIOSYNTHETIC PROTEIN / ALPHA DOMAIN / KAURENE CYCLIZATION / ENT-CPP
Function / homologyTerpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / Uncharacterized protein blr2150
Function and homology information
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsLiu, W. / Zheng, Y. / Huang, C.H. / Ko, T.P. / Guo, R.T.
CitationJournal: Sci Rep / Year: 2014
Title: Structure, function and inhibition of ent-kaurene synthase from Bradyrhizobium japonicum.
Authors: Liu, W. / Feng, X. / Zheng, Y. / Huang, C.H. / Nakano, C. / Hoshino, T. / Bogue, S. / Ko, T.P. / Chen, C.C. / Cui, Y. / Li, J. / Wang, I. / Hsu, S.T. / Oldfield, E. / Guo, R.T.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 14, 2015ID: 3W3F
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein blr2150
B: Uncharacterized protein blr2150


Theoretical massNumber of molelcules
Total (without water)66,8362
Polymers66,8362
Non-polymers00
Water11,241624
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-11 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.796, 65.796, 135.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Uncharacterized protein blr2150 / ORF8


Mass: 33417.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Gene: blr2150 / Plasmid: PET-42B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q45222
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.7M AMMONIUM TARTRATE DIBASIC PH 7.0, 2-4% W/V PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.92→25 Å / Num. obs: 43643 / % possible obs: 94.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 42.9
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.92→25 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3982 -RANDOM
Rwork0.191 ---
obs0.191 43643 94.8 %-
Refinement stepCycle: 1 / Resolution: 1.92→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4310 0 0 624 4934
LS refinement shellResolution: 1.92→1.99 Å
RfactorNum. reflection% reflection
Rfree0.232 3982 -
Rwork0.191 --
obs--94.8 %

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