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- PDB-4jig: Crystal structure of a putative dehydrogenase from Burkholderia c... -

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Basic information

Entry
Database: PDB / ID: 4jig
TitleCrystal structure of a putative dehydrogenase from Burkholderia cenocepacia
ComponentsDehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / National Institute for Allergy and Infectious Disease / NADP-dependent
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
Similarity search - Domain/homology
ACETATE ION / Putative dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative dehydrogenase from Burkholderia cenocepacia
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMar 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0514
Polymers26,8411
Non-polymers2103
Water2,738152
1
A: Dehydrogenase
hetero molecules

A: Dehydrogenase
hetero molecules

A: Dehydrogenase
hetero molecules

A: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,20616
Polymers107,3654
Non-polymers84112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area14250 Å2
ΔGint-75 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.890, 102.810, 123.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Dehydrogenase /


Mass: 26841.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BCAL2369, BceJ2315_23290 / Plasmid: pBG1861 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E5P7
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: BuceA.00010.a.B1 PS01733 at 22.8 mg/mL against JCSG+ screen condition D11, 140 mM CaCl2, 70 mM NaOAc pH 4.6, 14% isopropanol, 30% glycerol, crystal tracking ID 242030d11, unique puck ID smk5- ...Details: BuceA.00010.a.B1 PS01733 at 22.8 mg/mL against JCSG+ screen condition D11, 140 mM CaCl2, 70 mM NaOAc pH 4.6, 14% isopropanol, 30% glycerol, crystal tracking ID 242030d11, unique puck ID smk5-3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 20185 / Num. obs: 20122 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 27.516 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.4953.326566146199.5
1.9-1.950.4193.796448144699.7
1.95-2.010.3025.396232138699.6
2.01-2.070.2576.146044134999.9
2.07-2.140.217.55870130899.7
2.14-2.210.1579.975748127799.9
2.21-2.290.13411.275520123599.9
2.29-2.390.11512.715364119699.8
2.39-2.490.10314.2650891136100
2.49-2.620.08317.34918108899.9
2.62-2.760.06819.894754105799.9
2.76-2.930.05624.024319965100
2.93-3.130.04528.874204938100
3.13-3.380.03634.923864870100
3.38-3.70.02743.23353881199.8
3.7-4.140.02450.943127718100
4.14-4.780.0256.52281065799.4
4.78-5.850.02153.192442550100
5.85-8.270.01957.53189743799.5
8.270.01668.9895323790.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.74 Å
Translation3 Å19.74 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IQG

4iqg


Resolution: 1.85→19.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1733 / WRfactor Rwork: 0.1336 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8819 / SU B: 5.331 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1131 / SU Rfree: 0.1168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 1021 5.1 %RANDOM
Rwork0.1503 ---
obs0.1526 20060 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.48 Å2 / Biso mean: 25.6368 Å2 / Biso min: 13.84 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å2-0 Å2
2---1.59 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 14 152 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191717
X-RAY DIFFRACTIONr_bond_other_d0.0010.021669
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9712334
X-RAY DIFFRACTIONr_angle_other_deg0.83533794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0922.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18115251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5571519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
X-RAY DIFFRACTIONr_mcbond_it1.3791.98954
X-RAY DIFFRACTIONr_mcbond_other1.3491.977951
X-RAY DIFFRACTIONr_mcangle_it2.0222.9521188
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 92 -
Rwork0.182 1297 -
all-1389 -
obs--95.79 %
Refinement TLS params.Method: refined / Origin x: 19.7661 Å / Origin y: 10.3567 Å / Origin z: 15.4962 Å
111213212223313233
T0.0439 Å2-0.0205 Å20.0214 Å2-0.032 Å2-0.0138 Å2--0.0252 Å2
L0.1255 °2-0.0444 °2-0.0756 °2-0.3228 °20.0657 °2--0.2799 °2
S-0.0456 Å °0.043 Å °-0.009 Å °-0.0248 Å °0.0226 Å °0.0036 Å °0.0775 Å °0.0128 Å °0.0229 Å °

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