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- PDB-3f1k: Crystal Structure of yciK from E. coli, an oxidoreductase, comple... -

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Basic information

Entry
Database: PDB / ID: 3f1k
TitleCrystal Structure of yciK from E. coli, an oxidoreductase, complexed with NADP+ at 2.6A resolution
ComponentsUncharacterized oxidoreductase yciK
KeywordsOXIDOREDUCTASE / yciK / E. coli / NADP+
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity
Similarity search - Function
: / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized oxidoreductase YciK
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, SAD / MAD / Resolution: 2.6 Å
AuthorsVijayalakshmi, J. / Woodard, R.W.
CitationJournal: to be published
Title: Structure of an oxidoreductase, yciK from E. coli, in two crystal forms - NADP+ unbound structure at 0.95 A resolution
Authors: Vijayalakshmi, J. / Meredith, T.C. / Woodard, R.W.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized oxidoreductase yciK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0792
Polymers28,3361
Non-polymers7431
Water88349
1
A: Uncharacterized oxidoreductase yciK
hetero molecules

A: Uncharacterized oxidoreductase yciK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1594
Polymers56,6722
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area5460 Å2
ΔGint-31 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.509, 88.509, 80.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Uncharacterized oxidoreductase yciK


Mass: 28336.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K-12 MG1655 / Gene: b1271, JW1263, yciK / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31808, Oxidoreductases
#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.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium Acetate monohydrate pH 4.6, 8% w/v polyethylene glycol 4000, vapor diffusion, hanging drop, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D10.97887, 0.97864, 0.96860
SYNCHROTRONAPS 31-ID20.9799
Detector
TypeIDDetectorDateDetails
MAR CCD 300 mm1CCDNov 1, 2007Si(III) Monochromator
MAR CCD 165 mm2CCDNov 23, 2007Diamond (III) Monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(III) MonochromatorMADMx-ray1
2Diamond(III) MonochromatorSADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978871
20.978641
30.96861
40.97991
ReflectionRedundancy: 11.51 % / Number: 154252 / Rmerge(I) obs: 0.112 / Χ2: 1.9 / D res high: 2.46 Å / D res low: 40.28 Å / Num. obs: 13304 / % possible obs: 98.2
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
5.340.2898.80.1138.4710.39756
4.215.31000.0862.7811.71160
3.674.211000.0941.5111.96106
3.343.671000.1091.1111.9763
3.13.341000.158112.0835
2.923.11000.210.9312.0626
2.772.921000.2810.8612.0622
2.652.771000.3580.8312.099
2.552.651000.4380.7912.044
2.462.5582.90.450.768.241
ReflectionResolution: 2.5→44.25 Å / Num. obs: 12975 / % possible obs: 99.9 % / Redundancy: 21.76 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.114 / Χ2: 1 / Net I/σ(I): 16.6 / Scaling rejects: 2134
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.5-2.5921.40.4246.32748012821.06100
2.59-2.6922.280.3836.92829912671.05100
2.69-2.8222.260.2839.22850312761.04100
2.82-2.9622.260.24110.42868212840.97100
2.96-3.1522.250.19212.52865912840.93100
3.15-3.3922.190.14615.82882312940.89100
3.39-3.7322.010.10921.82854512910.89100
3.73-4.2721.830.09625.62858013010.95100
4.27-5.3821.840.08829.12870113110.97100
5.38-44.2519.490.09628.52823213851.2999.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
d*TREK9.3Ddata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD, SAD / Resolution: 2.6→35.608 Å / Occupancy max: 1 / Occupancy min: 0.77 / SU ML: 0.4 / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber
Details: SOME OF THE TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS INCLUDE FLEXIBLE TERMINAL RESIDUES
RfactorNum. reflection% reflection
Rfree0.261 2188 10.14 %
Rwork0.211 --
obs0.216 21570 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.25 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 163.25 Å2 / Biso mean: 58.194 Å2 / Biso min: 23.98 Å2
Baniso -1Baniso -2Baniso -3
1--3.711 Å2-0 Å20 Å2
2---3.711 Å20 Å2
3---7.423 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 48 49 2053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012044
X-RAY DIFFRACTIONf_angle_d1.4162780
X-RAY DIFFRACTIONf_chiral_restr0.082307
X-RAY DIFFRACTIONf_plane_restr0.007361
X-RAY DIFFRACTIONf_dihedral_angle_d20.705771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.6570.2991270.24812071334100
2.657-2.7180.2941360.22612171353100
2.718-2.7860.2591320.23112351367100
2.786-2.8620.3091380.22612031341100
2.862-2.9460.2771260.22412201346100
2.946-3.0410.2771340.22912221356100
3.041-3.1490.3371440.24212211365100
3.149-3.2760.3421380.26212061344100
3.276-3.4240.3221450.23912171362100
3.424-3.6050.331340.22712131347100
3.605-3.830.2781420.19312401382100
3.83-4.1260.1971380.18811991337100
4.126-4.540.231440.17211901334100
4.54-5.1950.2121360.16712281364100
5.195-6.5390.2281400.20412061346100
6.539-35.6110.1951340.1711158129295

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