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- PDB-3rc1: Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura ... -

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Basic information

Entry
Database: PDB / ID: 3rc1
TitleCrystal Structure of KijD10, a 3-ketoreductase from Actinomadura kijaniata incomplex with NADP and TDP-benzene
ComponentsSugar 3-ketoreductase
KeywordsSUGAR BINDING PROTEIN / sugar biosynthesis / ketoreductase / TDP binding / NADP binding
Function / homology
Function and homology information


dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose 3-reductase / antibiotic biosynthetic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / GFO/IDH/MocA C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...: / : / GFO/IDH/MocA C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / Chem-TLO / dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose 3-reductase
Similarity search - Component
Biological speciesActinomadura kijaniata (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsHolden, H.M. / Kubiak, R.L.
CitationJournal: Biochemistry / Year: 2011
Title: Combined Structural and Functional Investigation of a C-3''-Ketoreductase Involved in the Biosynthesis of dTDP-l-Digitoxose.
Authors: Kubiak, R.L. / Holden, H.M.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Sugar 3-ketoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7358
Polymers39,2621
Non-polymers1,4737
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.826, 104.154, 145.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sugar 3-ketoreductase


Mass: 39262.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura kijaniata (bacteria) / Gene: KijD10 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: B3TMR8

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Non-polymers , 7 types, 384 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-TLO / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine / thymidine diphosphate phenol


Mass: 478.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O11P2
#4: 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
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0 M sodium/potassium phosphate, 100 mM HEPPS, 5 mM NADP, 5 mM TDP-benzene, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 12, 2011 / Details: montel mirrors
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.71→84.65 Å / Num. all: 59618 / Num. obs: 59618 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.3
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.5 / Num. unique all: 8171 / Rsym value: 0.643 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0066refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model generated from binary structure, PDB entry 3RBV

3rbv


Resolution: 1.71→60 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.826 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23367 3008 5 %RANDOM
Rwork0.20367 ---
obs0.20518 56605 99.61 %-
all-56605 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.572 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.77 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.71→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 91 377 3036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212742
X-RAY DIFFRACTIONr_angle_refined_deg2.3621.9873746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48122.409137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38615412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791532
X-RAY DIFFRACTIONr_chiral_restr0.1790.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212144
X-RAY DIFFRACTIONr_mcbond_it1.9391.51629
X-RAY DIFFRACTIONr_mcangle_it2.77322618
X-RAY DIFFRACTIONr_scbond_it4.30831113
X-RAY DIFFRACTIONr_scangle_it6.2314.51125
LS refinement shellResolution: 1.71→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 232 -
Rwork0.287 4013 -
obs--96.52 %

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