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- PDB-3f4l: Crystal structure of a probable oxidoreductase yhhX in Triclinic ... -

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Basic information

Entry
Database: PDB / ID: 3f4l
TitleCrystal structure of a probable oxidoreductase yhhX in Triclinic form. Northeast Structural Genomics target ER647
ComponentsPutative oxidoreductase yhhX
KeywordsOXIDOREDUCTASE / oxidoreductase yhhX / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / cytosol
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta 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 ...Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta 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
Uncharacterized oxidoreductase YhhX
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSeetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative oxidoreductase yhhX
B: Putative oxidoreductase yhhX
C: Putative oxidoreductase yhhX
D: Putative oxidoreductase yhhX
E: Putative oxidoreductase yhhX
F: Putative oxidoreductase yhhX


Theoretical massNumber of molelcules
Total (without water)234,3216
Polymers234,3216
Non-polymers00
Water10,521584
1
A: Putative oxidoreductase yhhX
F: Putative oxidoreductase yhhX


Theoretical massNumber of molelcules
Total (without water)78,1072
Polymers78,1072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-6 kcal/mol
Surface area28240 Å2
MethodPISA
2
B: Putative oxidoreductase yhhX
C: Putative oxidoreductase yhhX


Theoretical massNumber of molelcules
Total (without water)78,1072
Polymers78,1072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-6 kcal/mol
Surface area28350 Å2
MethodPISA
3
D: Putative oxidoreductase yhhX
E: Putative oxidoreductase yhhX


Theoretical massNumber of molelcules
Total (without water)78,1072
Polymers78,1072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-5 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.189, 100.785, 102.166
Angle α, β, γ (deg.)114.40, 103.31, 101.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative oxidoreductase yhhX


Mass: 39053.418 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b3440, JW3403, yhhX / Production host: Escherichia coli (E. coli) / References: UniProt: P46853, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: NH4Cl, Tris pH 8, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 274347 / Num. obs: 274347 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.043 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.216 / Num. unique all: 28162 / % possible all: 93.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→42.6 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 125649.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 12361 4.8 %RANDOM
Rwork0.231 ---
obs0.231 257403 86.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9885 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å23.5 Å2-0.11 Å2
2---1.25 Å22.23 Å2
3----1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16386 0 0 584 16970
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 2069 4.7 %
Rwork0.286 41741 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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