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- PDB-1c1d: L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH N... -

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Basic information

Entry
Database: PDB / ID: 1c1d
TitleL-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE
Components(L-PHENYLALANINE ...Phenylalanine) x 2
KeywordsOXIDOREDUCTASE / AMINO 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
ISOPROPYL ALCOHOL / : / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PHENYLALANINE / PHOSPHATE ION / Phenylalanine dehydrogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsVanhooke, J.L. / Thoden, J.B.
CitationJournal: Biochemistry / Year: 2000
Title: Rhodococcus L-phenylalanine dehydrogenase: kinetics, mechanism, and structural basis for catalytic specificity.
Authors: Brunhuber, N.M. / Thoden, J.B. / Blanchard, J.S. / Vanhooke, J.L.
History
DepositionJul 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,87414
Polymers72,8552
Non-polymers2,01912
Water16,718928
1
A: L-PHENYLALANINE DEHYDROGENASE
hetero molecules

B: L-PHENYLALANINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,87414
Polymers72,8552
Non-polymers2,01912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area1960 Å2
ΔGint-10 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 110.600, 113.300
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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L-PHENYLALANINE ... , 2 types, 2 molecules AB

#1: Protein L-PHENYLALANINE DEHYDROGENASE


Mass: 36412.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Plasmid: PBL-1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q59771
#2: Protein L-PHENYLALANINE DEHYDROGENASE


Mass: 36442.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Plasmid: PBL-1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q59771

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Non-polymers , 7 types, 940 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 928 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growpH: 8.7 / Details: pH 8.70
Crystal grow
*PLUS
pH: 7.8 / Method: batch method / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlenzyme11
250 mMtriethanolamine11pH7.8
3100 mM11NaCl
410 mMNADH11
520 mML-phenylalanine11
62.55 Msodium potassium phosphate11
7100 mMCHES11pH8.7
84 %(v/v)2-propanol11

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.7433
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7433 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 216285 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.4
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 5 % / Rmerge(I) obs: 0.255 / % possible all: 92.1
Reflection
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Num. measured all: 1286363 / Biso Wilson estimate: 0 Å2
Reflection shell
*PLUS
% possible obs: 92.1 % / Num. unique obs: 20510 / Num. measured obs: 103853 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTV. 5-Ephasing
RefinementResolution: 1.25→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.238 21600 -TNT 5EB
Rwork0.193 ---
all0.195 215573 --
obs0.195 215573 96 %-
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 0 127 928 6079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.53
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d14.7
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.012

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