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- PDB-3edm: Crystal structure of a short chain dehydrogenase from Agrobacteri... -

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Basic information

Entry
Database: PDB / ID: 3edm
TitleCrystal structure of a short chain dehydrogenase from Agrobacterium tumefaciens
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / DEHYDROGENASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyPKS_KR / 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 / Short chain dehydrogenase
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Chang, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a short chain dehydrogenase from Agrobacterium tumefaciens
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Chang, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short chain dehydrogenase
B: Short chain dehydrogenase
C: Short chain dehydrogenase
D: Short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)107,6464
Polymers107,6464
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-49 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.501, 131.260, 67.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Short chain dehydrogenase


Mass: 26911.521 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Strain: C58 / Gene: AGR_L_3556, Atu3026 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CEK0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 22% PEG 3350, 200mM sodium formate, pH 7.0, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.3→43.783 Å / Num. all: 46266 / Num. obs: 46266 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.5 / Num. measured all: 54360 / Num. unique all: 6669 / Rsym value: 0.472 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
DENZOdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.776 / SU B: 6.627 / SU ML: 0.163 / SU R Cruickshank DPI: 0.273 / SU Rfree: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.273 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2311 5 %RANDOM
Rwork0.195 ---
obs0.198 46172 99.98 %-
all-46181 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 70.01 Å2 / Biso mean: 35.109 Å2 / Biso min: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å20 Å20 Å2
2--0.92 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6253 0 0 189 6442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226356
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9498608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48423.652230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95715976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0241539
X-RAY DIFFRACTIONr_chiral_restr0.0980.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024741
X-RAY DIFFRACTIONr_mcbond_it0.7861.54315
X-RAY DIFFRACTIONr_mcangle_it1.49326773
X-RAY DIFFRACTIONr_scbond_it2.58132041
X-RAY DIFFRACTIONr_scangle_it4.2064.51831
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 174 -
Rwork0.229 3138 -
all-3312 -
obs-3138 99.97 %

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