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- PDB-4dyv: Crystal structure of a short-chain dehydrogenase/reductase SDR fr... -

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Basic information

Entry
Database: PDB / ID: 4dyv
TitleCrystal structure of a short-chain dehydrogenase/reductase SDR from Xanthobacter autotrophicus Py2
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / 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
Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Phenix_autosol / Resolution: 1.8 Å
AuthorsAgarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Hillerich, B. / Kar, A. / Lafleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Hillerich, B. / Kar, A. / Lafleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. / Gizzi, A. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a short-chain dehydrogenase/reductase SDR from Xanthobacter autotrophicus Py2
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1402
Polymers29,1041
Non-polymers351
Water3,837213
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5608
Polymers116,4184
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area10320 Å2
ΔGint-114 kcal/mol
Surface area30490 Å2
MethodPISA
2
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2804
Polymers58,2092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area3400 Å2
ΔGint-48 kcal/mol
Surface area17010 Å2
MethodPISA
3
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2804
Polymers58,2092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2090 Å2
ΔGint-33 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.901, 83.046, 93.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 29104.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: ATCC BAA-1158 / Py2 / Gene: Xaut_2039 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: A7IGZ0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na-acetate trihydrate, pH 4.6, 8% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 29, 2012 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 26195 / Num. obs: 26195 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8 / Num. unique all: 2501 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CBASSdata collection
AutoSolphasing
Cootmodel building
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: Phenix_autosol / Resolution: 1.8→35.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.753 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20456 1325 5.1 %RANDOM
Rwork0.16607 ---
obs0.16799 24806 99.58 %-
all-26195 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 1 213 1751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0221561
X-RAY DIFFRACTIONr_angle_refined_deg2.3311.9572127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40924.21157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53515235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.489159
X-RAY DIFFRACTIONr_chiral_restr0.1920.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211170
X-RAY DIFFRACTIONr_mcbond_it1.5471.51053
X-RAY DIFFRACTIONr_mcangle_it2.47221684
X-RAY DIFFRACTIONr_scbond_it3.853508
X-RAY DIFFRACTIONr_scangle_it5.7134.5443
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 103 -
Rwork0.21 1766 -
obs--97.55 %

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