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- PDB-3sc4: Crystal structure of a Short chain dehydrogenase (A0QTM2 homolog)... -

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Basic information

Entry
Database: PDB / ID: 3sc4
TitleCrystal structure of a Short chain dehydrogenase (A0QTM2 homolog) Mycobacterium thermoresistibile
ComponentsShort chain dehydrogenase (A0QTM2 homolog)
KeywordsOXIDOREDUCTASE / SSGCID / NIH / NIAID / SBRI / UW / Emerald BioStructures / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Unknown ligand / Short chain dehydrogenase
Function and homology information
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a Short chain dehydrogenase (A0QTM2 homolog) Mycobacterium thermoresistibile
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Gardberg, A. / Clifton, M.C. / Staker, B. / Stewart, L.
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Short chain dehydrogenase (A0QTM2 homolog)
B: Short chain dehydrogenase (A0QTM2 homolog)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,49920
Polymers59,8942
Non-polymers60518
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-112 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.490, 111.490, 124.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4 / Auth seq-ID: 1 - 400 / Label seq-ID: 1 - 400

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Short chain dehydrogenase (A0QTM2 homolog)


Mass: 29947.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G7CNA1*PLUS

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Non-polymers , 6 types, 168 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 5 / Source method: obtained synthetically
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Internal tracking number 220646H3. Focus screen based on JCSG E2. 2 M ammonium sulfate, 0.1 M cacodylate, pH 6.54, 200 mM sodium chloride. MythA.01365.a.A1 PW28688 at 27.8 mg/mL, VAPOR ...Details: Internal tracking number 220646H3. Focus screen based on JCSG E2. 2 M ammonium sulfate, 0.1 M cacodylate, pH 6.54, 200 mM sodium chloride. MythA.01365.a.A1 PW28688 at 27.8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2011
RadiationMonochromator: Asymmetric curved crystal, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.5→48.28 Å / Num. all: 30482 / Num. obs: 30423 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 37.017 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 21.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.5-2.569.20.5644.42068622402240100
2.56-2.640.4655.4203622182100
2.64-2.710.4396.2197352145100
2.71-2.80.3387.3195022063100
2.8-2.890.2848.9192392021100
2.89-2.990.2310.8183571932100
2.99-3.10.16814.3178661875100
3.1-3.230.13617.4170201786100
3.23-3.370.10920.7166291746100
3.37-3.540.09625.514871163299.5
3.54-3.730.08229.413984158398.9
3.73-3.950.06634.212736145598.2
3.95-4.230.05437.4130451382100
4.23-4.560.04744.3123171307100
4.56-50.04644.6113721209100
5-5.590.0541.2102251099100
5.59-6.460.05437.78745956100
6.46-7.910.03847.57805821100
7.91-11.180.02762.76066640100
11.180.02660.5325534998.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.28 Å
Translation2.5 Å48.28 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KVO

3kvo


Resolution: 2.5→48.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.29 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2343 7.7 %RANDOM
Rwork0.178 ---
obs0.181 30393 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.608 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.22 Å20 Å2
2---0.45 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 30 150 4293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224246
X-RAY DIFFRACTIONr_bond_other_d0.0010.022824
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9895797
X-RAY DIFFRACTIONr_angle_other_deg0.90636946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39824.211152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98415667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2571526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
X-RAY DIFFRACTIONr_mcbond_it0.6061.52815
X-RAY DIFFRACTIONr_mcbond_other0.1221.51149
X-RAY DIFFRACTIONr_mcangle_it1.15324520
X-RAY DIFFRACTIONr_scbond_it1.83731431
X-RAY DIFFRACTIONr_scangle_it3.0524.51273
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3357 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.240.5
MEDIUM THERMAL0.462
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 157 -
Rwork0.258 2073 -
all-2230 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.55680.6633-0.29311.1193-0.2941.01190.0299-0.2498-0.09530.0655-0.12180.0120.05070.02340.0920.0091-0.01280.01020.0478-0.01460.083429.512-35.63334.774
20.83890.3246-0.56131.2132-0.29841.2865-0.06790.07810.0619-0.2307-0.0102-0.05870.0751-0.06380.07810.05270.00230.00170.0116-0.00880.075840.242-24.3774.082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 281
2X-RAY DIFFRACTION2B1 - 281

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