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- PDB-5hws: Crystal structure of ketopantoate reductase from Thermococcus kod... -

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Basic information

Entry
Database: PDB / ID: 5hws
TitleCrystal structure of ketopantoate reductase from Thermococcus kodakarensis complexed with NADP+
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / NADP / Rossmann type fold
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / coenzyme A biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAikawa, Y. / Nishitani, Y. / Miki, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
CREST/JST Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of ketopantoate reductase from Thermococcus kodakarensis complexed with NADP+
Authors: Aikawa, Y. / Nishitani, Y. / Tomita, H. / Atomi, H. / Miki, K.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-dehydropantoate 2-reductase
B: 2-dehydropantoate 2-reductase
C: 2-dehydropantoate 2-reductase
D: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,2018
Polymers136,2274
Non-polymers2,9744
Water6,179343
1
A: 2-dehydropantoate 2-reductase
D: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6004
Polymers68,1142
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-23 kcal/mol
Surface area24070 Å2
MethodPISA
2
B: 2-dehydropantoate 2-reductase
C: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6004
Polymers68,1142
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-23 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.616, 44.944, 183.286
Angle α, β, γ (deg.)84.93, 87.83, 65.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
2-dehydropantoate 2-reductase / Ketopantoate reductase


Mass: 34056.770 Da / Num. of mol.: 4 / Mutation: C84A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1968 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q5JGC2, 2-dehydropantoate 2-reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, 2-propanol, sodium acetate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42722 / % possible obs: 88.4 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 29.2 Å2 / Net I/σ(I): 9.4
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.1 / % possible all: 79.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AYV

5ayv


Resolution: 2.3→45.642 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 2164 5.07 %Random selection
Rwork0.2218 ---
obs0.2237 42722 88.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9282 0 192 343 9817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049662
X-RAY DIFFRACTIONf_angle_d0.81513151
X-RAY DIFFRACTIONf_dihedral_angle_d14.4053469
X-RAY DIFFRACTIONf_chiral_restr0.0361492
X-RAY DIFFRACTIONf_plane_restr0.0041661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2966-2.350.31651480.27982361X-RAY DIFFRACTION75
2.35-2.40880.32511320.28112559X-RAY DIFFRACTION86
2.4088-2.47390.32341460.26972826X-RAY DIFFRACTION91
2.4739-2.54670.32661390.27592733X-RAY DIFFRACTION90
2.5467-2.62890.29911470.2732784X-RAY DIFFRACTION89
2.6289-2.72290.30271450.26392639X-RAY DIFFRACTION88
2.7229-2.83190.31691390.27122668X-RAY DIFFRACTION86
2.8319-2.96070.30771410.24992608X-RAY DIFFRACTION86
2.9607-3.11680.321470.24452826X-RAY DIFFRACTION92
3.1168-3.3120.28591410.24152767X-RAY DIFFRACTION91
3.312-3.56770.23521500.222765X-RAY DIFFRACTION90
3.5677-3.92650.25041380.19882642X-RAY DIFFRACTION86
3.9265-4.49420.22391750.17952869X-RAY DIFFRACTION93
4.4942-5.66060.20511490.18342656X-RAY DIFFRACTION87
5.6606-45.65110.19671270.18262855X-RAY DIFFRACTION92

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