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- PDB-1bxg: PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD... -

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Basic information

Entry
Database: PDB / ID: 1bxg
TitlePHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND BETA-PHENYLPROPIONATE
Components(PHENYLALANINE ...) x 2
KeywordsAMINO ACID DEHYDROGENASE / OXIDATIVE DEAMINATION MECHANISM
Function / homology
Function and homology information


phenylalanine dehydrogenase / phenylalanine dehydrogenase activity / L-phenylalanine biosynthetic process / L-phenylalanine catabolic process / nucleotide binding
Similarity search - Function
Glutamate/phenylalanine/leucine/valine dehydrogenase, bacterial/archaeal / Leucine Dehydrogenase, chain A, domain 1 / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Glutamate/phenylalanine/leucine/valine dehydrogenase, bacterial/archaeal / Leucine Dehydrogenase, chain A, domain 1 / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROCINNAMIC ACID / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Phenylalanine dehydrogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsVanhooke, J.L. / Thoden, J.B. / Brunhuber, N.M.W. / Blanchard, J.L. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1999
Title: Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism.
Authors: Vanhooke, J.L. / Thoden, J.B. / Brunhuber, N.M. / Blanchard, J.S. / Holden, H.M.
History
DepositionOct 2, 1998-
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHENYLALANINE DEHYDROGENASE
B: PHENYLALANINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9778
Polymers73,2162
Non-polymers1,7616
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.510, 116.960, 111.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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PHENYLALANINE ... , 2 types, 2 molecules AB

#1: Protein PHENYLALANINE DEHYDROGENASE /


Mass: 36571.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Cell line: BL21 / Plasmid: PBL-1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q59771, phenylalanine dehydrogenase
#2: Protein PHENYLALANINE DEHYDROGENASE /


Mass: 36643.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Cell line: BL21 / Plasmid: PBL-1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q59771, phenylalanine dehydrogenase

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Non-polymers , 5 types, 181 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-HCI / HYDROCINNAMIC ACID / 3PP / 3-PHENYLPROPIONIC ACID / Phenylpropanoic acid


Mass: 150.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growpH: 8.7 / Details: pH 8.7
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
210 mMNAD+1drop
32.70 Msodium potassium phosphate1drop
4100 mMCHES1drop
510 mMbeta-phenylpropionate1drop
64 %(v/v)2-propanol1drop

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1998 / Details: GOBEL MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 34077 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 6.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.25 / % possible all: 72
Reflection
*PLUS
Num. measured all: 73548
Reflection shell
*PLUS
% possible obs: 72 % / Num. unique obs: 3428 / Num. measured obs: 5120

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Processing

Software
NameVersionClassification
TNT5Erefinement
XDSdata reduction
XCALIBREdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.17 --
all0.17 34077 -
obs-34077 88 %
Solvent computationBsol: 589.8 Å2 / ksol: 1.114 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 116 175 5318
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01380053
X-RAY DIFFRACTIONt_angle_deg2.467105805
X-RAY DIFFRACTIONt_dihedral_angle_d15.97751700
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.00812010
X-RAY DIFFRACTIONt_gen_planes0.008148720
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.0710810
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.9770
X-RAY DIFFRACTIONt_planar_d0.00810
X-RAY DIFFRACTIONt_plane_restr0.00820

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