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- PDB-4xly: The complex structure of KS-D75C with substrate CPP -

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Basic information

Entry
Database: PDB / ID: 4xly
TitleThe complex structure of KS-D75C with substrate CPP
ComponentsUncharacterized protein blr2150
KeywordsHYDROLASE / Diterpene synthases
Function / homologyTerpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / Chem-ECP / Uncharacterized protein blr2150
Function and homology information
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsHu, Y. / Zheng, Y. / Ko, T.P. / Liu, W. / 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
DepositionJan 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7134
Polymers66,8122
Non-polymers9012
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-12 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.814, 65.814, 136.244
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: 33406.051 Da / Num. of mol.: 2 / Mutation: D75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) (bacteria)
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: blr2150 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21trxB(DE3) / References: UniProt: Q45222
#2: Chemical ChemComp-ECP / (2E)-3-methyl-5-[(1R,4aR,8aR)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate


Mass: 450.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H36O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M ammonium tartrate dibasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→25 Å / Num. obs: 51614 / % possible obs: 99.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 42.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5123 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W3F

3w3f
PDB Unreleased entry


Resolution: 1.82→25 Å / Cross valid method: FREE R-VALUE / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3582 -RANDOM
Rwork0.2 66780 --
all-51739 --
obs-50837 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.82→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 58 376 4537
LS refinement shellResolution: 1.8→1.9 Å /
RfactorNum. reflection
Rfree0.31 -
Rwork0.28 -
obs-3310

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