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- PDB-4kwh: The crystal structure of angucycline C-6 ketoreductase LanV with ... -

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Basic information

Entry
Database: PDB / ID: 4kwh
TitleThe crystal structure of angucycline C-6 ketoreductase LanV with bound NADP
ComponentsReductase homolog
KeywordsOXIDOREDUCTASE / Rossmann fold / ketoreductase / NADPH
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / Reductase homolog
Similarity search - Component
Biological speciesStreptomyces cyanogenus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsPaananen, P. / Patrikainen, P. / Kallio, P. / Mantsala, P. / Niemi, J. / Niiranen, L. / Metsa-Ketela, M.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and functional analysis of angucycline C-6 ketoreductase LanV involved in landomycin biosynthesis.
Authors: Paananen, P. / Patrikainen, P. / Kallio, P. / Mantsala, P. / Niemi, J. / Niiranen, L. / Metsa-Ketela, M.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Sep 20, 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: Reductase homolog
B: Reductase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8218
Polymers55,0022
Non-polymers1,8196
Water8,017445
1
A: Reductase homolog
B: Reductase homolog
hetero molecules

A: Reductase homolog
B: Reductase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,64316
Polymers110,0044
Non-polymers3,63812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area18620 Å2
ΔGint-92 kcal/mol
Surface area34640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.500, 92.500, 106.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Reductase homolog


Mass: 27501.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cyanogenus (bacteria) / Gene: lanV / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9ZGC1
#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-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 0.1M Bis-Tris-Propane, 0.2M sodium acetate, 18% PEG3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2011 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.65→46 Å / Num. obs: 56150 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 26.04 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 27.19
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 4.05 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ICC

3icc


Resolution: 1.7→46 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.129 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0956 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2597 5.1 %RANDOM
Rwork0.147 ---
obs0.149 51201 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å2-0 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 118 445 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024004
X-RAY DIFFRACTIONr_bond_other_d0.0030.022630
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9985458
X-RAY DIFFRACTIONr_angle_other_deg0.9813.0126411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0495539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20323.179151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21315614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2141534
X-RAY DIFFRACTIONr_chiral_restr0.1870.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02823
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 201 -
Rwork0.17 3247 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68390.11130.18780.4840.09590.43590.00360.0579-0.019-0.03280.0202-0.0991-0.0335-0.0002-0.02380.0239-0.00390.00760.0275-0.01070.022823.1914-0.131225.7325
20.52630.10040.06240.70710.16920.3109-0.0265-0.04560.1353-0.01070.02350.0402-0.02890.00740.0030.03170.0123-0.00350.0231-0.01390.0371.258621.936330.3115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 253
2X-RAY DIFFRACTION2B-3 - 253

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