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- PDB-3baz: Structure of hydroxyphenylpyruvate reductase from coleus blumei i... -

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Basic information

Entry
Database: PDB / ID: 3baz
TitleStructure of hydroxyphenylpyruvate reductase from coleus blumei in complex with NADP+
ComponentsHydroxyphenylpyruvate reductase
KeywordsOXIDOREDUCTASE / Pyruvate
Function / homology
Function and homology information


hydroxyphenylpyruvate reductase / : / hydroxyphenylpyruvate reductase activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Hydroxyphenylpyruvate reductase
Similarity search - Component
Biological speciesSolenostemon scutellarioides (plant)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 2.2 Å
AuthorsJaniak, V. / Klebe, G. / Petersen, M. / Heine, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth
Authors: Janiak, V. / Petersen, M. / Zentgraf, M. / Klebe, G. / Heine, A.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Hydroxyphenylpyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0812
Polymers36,3381
Non-polymers7431
Water2,594144
1
A: Hydroxyphenylpyruvate reductase
hetero molecules

A: Hydroxyphenylpyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1624
Polymers72,6762
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7520 Å2
ΔGint-39.9 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 63.500, 222.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-638-

HOH

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Components

#1: Protein Hydroxyphenylpyruvate reductase / HPPR


Mass: 36337.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solenostemon scutellarioides (plant) / Gene: hppr / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q65CJ7, hydroxyphenylpyruvate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG1000, 0.1M Imidazol, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 23761 / Num. obs: 23761 / % possible obs: 98.1 % / Redundancy: 12.3 % / Rsym value: 0.099 / Net I/σ(I): 24.3
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1281 / Rsym value: 0.559 / % possible all: 81.4

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 3BA1

3ba1


Resolution: 2.2→10 Å / Num. parameters: 10285 / Num. restraintsaints: 9957 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 1065 -RANDOM
Rwork0.2107 ---
obs0.2107 21191 93.4 %-
all-22256 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2567.5
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 48 144 2568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0226
X-RAY DIFFRACTIONs_zero_chiral_vol0.025
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0

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