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- PDB-3w21: Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygena... -

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Basic information

Entry
Database: PDB / ID: 3w21
TitleCrystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD
ComponentsPutative uncharacterized protein
KeywordsOXIDOREDUCTASE / DSBH fold / Dioxygenase / Zn / alpha-KG binding
Function / homologyq2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / 2-OXOGLUTARIC ACID / Prolyl 4-hydroxylase alpha subunit Fe(2+) 2OG dioxygenase domain-containing protein
Function and homology information
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsQin, H.M. / Miyakawa, T. / Jia, M.Z. / Nakamura, A. / Ohtsuka, J. / Xue, Y.L. / Kawashima, T. / Kasahara, T. / Hibi, M. / Ogawa, J. / Tanokura, M.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD
Authors: Qin, H.M. / Miyakawa, T. / Jia, M.Z. / Nakamura, A. / Ohtsuka, J. / Xue, Y.L. / Kawashima, T. / Kasahara, T. / Hibi, M. / Ogawa, J. / Tanokura, M.
History
DepositionNov 26, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6225
Polymers62,3452
Non-polymers2773
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-94 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.593, 71.143, 147.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein


Mass: 31172.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: ATCC BAA-244 / AMMD / Gene: Bamb_6045 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q0B2N4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1M CHES, 30%(w/v) PEG3000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 37009 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.056 / Net I/σ(I): 56.3
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 6.5 % / Num. unique all: 1808 / Rsym value: 0.252 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→32.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.744 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE SEMET SUBSTITUTES OF SADA WAS USED AS A STARTING MODEL. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27772 1827 5 %RANDOM
Rwork0.21174 ---
obs0.21507 34774 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.98→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 12 138 4092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194052
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.9585488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4625503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6923.547203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.95715614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6461536
X-RAY DIFFRACTIONr_chiral_restr0.1940.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213145
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 122 -
Rwork0.243 2319 -
obs--98.15 %

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