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- PDB-2ofp: Crystal structure of Escherichia coli ketopantoate reductase in a... -

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Basic information

Entry
Database: PDB / ID: 2ofp
TitleCrystal structure of Escherichia coli ketopantoate reductase in a ternary complex with NADP+ and pantoate
ComponentsKetopantoate reductase
KeywordsOXIDOREDUCTASE / panE / APBA / ketopantoate reductase / ternary complex
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP 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
ACETATE ION / 1,4-DIETHYLENE DIOXIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PANTOATE / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCiulli, A. / Chirgadze, D.Y. / Smith, A.G. / Blundell, T.L. / Abell, C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of Escherichia coli Ketopantoate Reductase in a Ternary Complex with NADP+ and Pantoate Bound: SUBSTRATE RECOGNITION, CONFORMATIONAL CHANGE, AND COOPERATIVITY.
Authors: Ciulli, A. / Chirgadze, D.Y. / Smith, A.G. / Blundell, T.L. / Abell, C.
History
DepositionJan 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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: Ketopantoate reductase
B: Ketopantoate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,86611
Polymers71,6742
Non-polymers2,1939
Water9,152508
1
A: Ketopantoate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9045
Polymers35,8371
Non-polymers1,0674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ketopantoate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9636
Polymers35,8371
Non-polymers1,1265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.692, 101.692, 171.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35836.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: panE, apbA / Plasmid: mini-pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P0A9J4, 2-dehydropantoate 2-reductase

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Non-polymers , 5 types, 517 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-PAF / PANTOATE / 2,4-DIHYDROXY-3,3-DIMETHYL-BUTYRATE / Pantoic acid


Mass: 147.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O4
#4: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 50mM HEPES-HCl, 35% v/v dioxane, 2 mM NADP+, 10 mM pantoate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 40670 / Num. obs: 40629 / % possible obs: 99.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.425 / Num. unique all: 40629 / Rsym value: 0.425 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1KS9 and 1YJQ

1ks9

1yjq


Resolution: 2.3→43.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.821 / SU ML: 0.12 / Isotropic thermal model: restrained isotropic / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFMAC 5.2.0019 and CNS v1.1 were used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2032 5 %RANDOM
Rwork0.15621 ---
obs0.1592 38533 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.301 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 144 508 5355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214955
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9796776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9755606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21924.454229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25315816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4311535
X-RAY DIFFRACTIONr_chiral_restr0.0950.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023731
X-RAY DIFFRACTIONr_nbd_refined0.2020.22412
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2479
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.219
X-RAY DIFFRACTIONr_mcbond_it3.0453087
X-RAY DIFFRACTIONr_mcangle_it4.14964861
X-RAY DIFFRACTIONr_scbond_it3.97252125
X-RAY DIFFRACTIONr_scangle_it5.3857.51915
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 143 -
Rwork0.182 2791 -
obs-2934 100 %

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