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- PDB-3db2: Crystal structure of a putative nadph-dependent oxidoreductase (d... -

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Basic information

Entry
Database: PDB / ID: 3db2
TitleCrystal structure of a putative nadph-dependent oxidoreductase (dhaf_2064) from desulfitobacterium hafniense dcb-2 at 1.70 A resolution
Componentsputative NADPH-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Two domain protein / rossmann fold / putative dehydrogenase / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity
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
Oxidoreductase domain protein / :
Similarity search - Component
Biological speciesDesulfitobacterium hafniense DCB-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative NADPH-dependent oxidoreductase (ZP_01370612.1) from DESULFITOBACTERIUM HAFNIENSE DCB-2 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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: putative NADPH-dependent oxidoreductase
B: putative NADPH-dependent oxidoreductase
C: putative NADPH-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9145
Polymers119,7303
Non-polymers1842
Water10,773598
1
C: putative NADPH-dependent oxidoreductase
hetero molecules

C: putative NADPH-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1886
Polymers79,8202
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area3780 Å2
ΔGint-22 kcal/mol
Surface area25390 Å2
MethodPISA
2
A: putative NADPH-dependent oxidoreductase
B: putative NADPH-dependent oxidoreductase


Theoretical massNumber of molelcules
Total (without water)79,8202
Polymers79,8202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-22 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.616, 104.616, 173.372
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein putative NADPH-dependent oxidoreductase


Mass: 39909.992 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense DCB-2 (bacteria)
Gene: ZP_01370612.1, Dhaf_4026 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q18XG3, UniProt: B8FRW3*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.2946.23THE STRUCTURE WAS PHASED BY MAD METHOD USING A CRYSTAL AT 2.4 A REMARK 200 RESOLUTION AND REFINED AGAINST A DIFFERENT CRYSTAL AT 1.7 A RESOLUTION.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop, nanodrop8.860.17M sodium acetate, 29.6% polyethylene glycol 4000, 15.0% Glycerol, 0.1M TRIS pH 8.86, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
2772vapor diffusion, sitting drop, nanodrop8.1415.0% Glycerol, 26.7% polyethylene glycol 4000, 0.17M sodium acetate, 0.1M TRIS pH 8.14, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL1-510.978791
SYNCHROTRONSSRL BL11-120.91837,0.97956
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDFeb 17, 20081m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing
MARMOSAIC 325 mm CCD2CCDJan 22, 2008Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9787911
20.918371
30.979561
ReflectionResolution: 1.7→29.748 Å / Num. obs: 120878 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.743.80.77213264587030.77299.3
1.74-1.797.40.74816358386310.748100
1.79-1.8410.80.6741.19111484010.674100
1.84-1.910.80.4841.58869581790.484100
1.9-1.9610.80.3452.28560678950.345100
1.96-2.0310.80.2538324376810.25100
2.03-2.1110.80.2023.78045174350.202100
2.11-2.1910.80.1694.37715871240.169100
2.19-2.2910.80.1494.87389568480.149100
2.29-2.410.80.1325.47081265710.132100
2.4-2.5310.70.11866723162620.118100
2.53-2.6910.70.1056.66332759170.105100
2.69-2.8710.60.0897.75929955690.089100
2.87-3.110.60.088.55513952160.08100
3.1-3.410.50.088.25060548150.08100
3.4-3.810.20.0837.94441343720.083100
3.8-4.399.60.0827.93740238770.082100
4.39-5.3810.10.0699.23318432950.069100
5.38-7.610.70.0679.82797126160.067100
7.6-29.769.60.06110.51414014710.06197.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXL-97refinement
PHENIXrefinement
SHELXphasing
SHELXrefinement
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
MolProbity3beta29model building
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.748 Å / Num. parameters: 34792 / Num. restraintsaints: 62193 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 4. THE DIFFRACTION DATA IS TWINNED WITH THE TWINNING OPERATOR "-H,-K,L" AND THE REFINED TWIN FRACTION IS 0.407.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 6076 5 %RANDOM
all0.142 120817 --
obs0.14 120817 100 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 29.353 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7986 0 12 598 8596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.043
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.074
X-RAY DIFFRACTIONs_approx_iso_adps0

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