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- PDB-3b1f: Crystal structure of prephenate dehydrogenase from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 3b1f
TitleCrystal structure of prephenate dehydrogenase from Streptococcus mutans
ComponentsPutative prephenate dehydrogenase
KeywordsOXIDOREDUCTASE / enzyme / prephenate / 4-hydroxyphenylpyruvate / oxidative decarboxylation pathway / tyrosine biosynthesis
Function / homology
Function and homology information


prephenate dehydrogenase / prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / membrane => GO:0016020 / nucleotide binding
Similarity search - Function
6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle ...6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative prephenate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKu, H.K. / Do, N.H. / Song, J.S. / Choi, S. / Shin, M.H. / Kim, K.J. / Lee, S.J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2011
Title: Crystal structure of prephenate dehydrogenase from Streptococcus mutans.
Authors: Ku, H.K. / Do, N.H. / Song, J.S. / Choi, S. / Yeon, S.H. / Shin, M.H. / Kim, K.J. / Park, S.R. / Park, I.Y. / Kim, S.K. / Lee, S.J.
History
DepositionJul 2, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2612
Polymers32,5981
Non-polymers6631
Water1,964109
1
A: Putative prephenate dehydrogenase
hetero molecules

A: Putative prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5234
Polymers65,1962
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area8500 Å2
ΔGint-71 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.340, 145.624, 77.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative prephenate dehydrogenase


Mass: 32598.061 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: SMU_781 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DUW0, prephenate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.44 Å3/Da / Density % sol: 64.2 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→52.7 Å / Num. obs: 24626

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→36.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.988 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23401 1314 5.1 %RANDOM
Rwork0.19324 ---
obs0.19531 24626 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.404 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 44 109 2391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9763152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6315284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88624.135104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7221514
X-RAY DIFFRACTIONr_chiral_restr0.1270.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211728
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_it1.5341.51422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45622285
X-RAY DIFFRACTIONr_scbond_it4.2093902
X-RAY DIFFRACTIONr_scangle_it5.9144.5867
X-RAY DIFFRACTIONr_rigid_bond_restr2.65232324
X-RAY DIFFRACTIONr_sphericity_free12.0543111
X-RAY DIFFRACTIONr_sphericity_bonded5.15832278
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 71 -
Rwork0.251 1553 -
obs--83.8 %
Refinement TLS params.Method: refined / Origin x: 29.3647 Å / Origin y: 19.6273 Å / Origin z: 36.7441 Å
111213212223313233
T0.1021 Å2-0.0197 Å2-0.0112 Å2-0.1667 Å20.0127 Å2--0.1259 Å2
L1.2824 °2-1.0738 °2-0.1674 °2-3.5211 °20.0255 °2--0.2905 °2
S0.0423 Å °0.0858 Å °0.2268 Å °-0.1568 Å °-0.0124 Å °0.279 Å °-0.0248 Å °-0.1093 Å °-0.0299 Å °

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