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- PDB-3dzb: Crystal structure of Prephenate dehydrogenase from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 3dzb
TitleCrystal structure of Prephenate dehydrogenase from Streptococcus thermophilus
ComponentsPrephenate dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / domain swap / 11134a2 / PSI2 / NYSGXRC / tyrosine biosynthesis / Ec:1.3.12.- / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / OXIDOREDUCTASE
Function / homology
Function and homology information


prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process
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
Prephenate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus thermophilus LMG 18311 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsZhang, Z. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Prephenate dehydrogenase from Streptococcus thermophilus
Authors: Zhang, Z. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prephenate dehydrogenase
B: Prephenate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)71,5562
Polymers71,5562
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-77 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.906, 145.005, 56.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Prephenate dehydrogenase /


Mass: 35778.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus LMG 18311 (bacteria)
Gene: tyrA, stu0642 / Plasmid: BC-pSGX3(BC), TOP10-invitrogen / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-Codon+RIL-stratagene / References: UniProt: Q5M554, prephenate dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M Potassium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. all: 25463 / Num. obs: 25463 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.8
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.709 / Num. unique all: 2491 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.46→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 935 -RANDOM
Rwork0.234 ---
all0.271 24324 --
obs0.271 24324 95.4 %-
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.2 Å20 Å20 Å2
2---6.66 Å20 Å2
3---1.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.46→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4439 0 0 60 4499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shellResolution: 2.46→2.57 Å / Rfactor Rfree error: 0.037
RfactorNum. reflection% reflection
Rfree0.376 105 -
Rwork0.31 --
obs-2438 58 %

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