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- PDB-4kzp: Crystal Structure of a Putative Short Chain Dehydrogenase from My... -

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Basic information

Entry
Database: PDB / ID: 4kzp
TitleCrystal Structure of a Putative Short Chain Dehydrogenase from Mycobacterium smegmatis
ComponentsOxidoreductase, short chain dehydrogenase/reductase family protein
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / reductase
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
Oxidoreductase, short chain dehydrogenase/reductase family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of a Putative Short Chain Dehydrogenase from Mycobacterium smegmatis
Authors: Dranow, D.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
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

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, short chain dehydrogenase/reductase family protein
B: Oxidoreductase, short chain dehydrogenase/reductase family protein
C: Oxidoreductase, short chain dehydrogenase/reductase family protein
D: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,51721
Polymers131,3424
Non-polymers1,17517
Water20,2311123
1
A: Oxidoreductase, short chain dehydrogenase/reductase family protein
D: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,35212
Polymers65,6712
Non-polymers68110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-36 kcal/mol
Surface area21150 Å2
MethodPISA
2
B: Oxidoreductase, short chain dehydrogenase/reductase family protein
C: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1659
Polymers65,6712
Non-polymers4957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-47 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.700, 86.070, 92.330
Angle α, β, γ (deg.)90.00, 103.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxidoreductase, short chain dehydrogenase/reductase family protein / / Short-chain dehydrogenase/reductase SDR


Mass: 32835.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5903, MSMEI_5743 / Production host: Escherichia coli (E. coli)
References: UniProt: A0R4P1, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 1123 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1M BisTris-HCl, pH=6.5 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2012
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. all: 148600 / Num. obs: 146223 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.68-1.720.462.94190
1.72-1.770.43.8198.5
1.77-1.820.3384.65198.6
1.82-1.880.2526.04198.7
1.88-1.940.1967.62198.9
1.94-2.010.1649.24198.8
2.01-2.080.12711.48199.1
2.08-2.170.09614.76199.1
2.17-2.270.07917.2199.1
2.27-2.380.06520.01199.2
2.38-2.50.05523.34199.3
2.5-2.660.04926.22199.5
2.66-2.840.04130.7199.5
2.84-3.070.03436.12199.5
3.07-3.360.02941.83199.9
3.36-3.760.02450.14199.8
3.76-4.340.02354.62199.8
4.34-5.310.0256.71199.7
5.31-7.510.0254.59199.7
7.510.01859.06197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.68 Å46.39 Å
Translation1.68 Å46.39 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QLJ

3qlj


Resolution: 1.68→46.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.04 / SU B: 3.454 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20526 7331 5 %RANDOM
Rwork0.17624 ---
obs0.17769 138868 98.48 %-
all-148439 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å20.89 Å2
2---1.77 Å2-0 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.68→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8276 0 76 1123 9475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198628
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.95911762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46251212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70723.612335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.066151249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5571567
X-RAY DIFFRACTIONr_chiral_restr0.0890.21398
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216579
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.721.1624699
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2251.7345876
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0791.2623929
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 511 -
Rwork0.238 9320 -
obs--90.03 %
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)
10.68440.43670.06160.5281-0.03890.23920.00570.00050.0337-0.0002-0.0104-0.0451-0.03420.04240.00470.0776-0.01210.00130.0730.00030.067329.472213.716222.2858
21.00090.5024-0.29590.422-0.24280.53570.1916-0.23540.11350.2209-0.12140.0234-0.11750.0065-0.07020.1563-0.03370.01210.0941-0.01640.036816.138810.358138.9098
31.03090.4977-0.07840.6255-0.11010.1772-0.0075-0.02920.15980.0424-0.0101-0.0208-0.03210.03980.01760.0756-0.0123-0.01210.0651-0.00530.070216.730913.621965.0671
41.33390.5825-0.87690.5423-0.64210.86370.1556-0.32920.22480.1562-0.07210.0373-0.10040.1274-0.08350.1674-0.0490.01680.1394-0.08110.05363.4988.448382.8144
50.50090.3093-0.14380.6749-0.03270.2626-0.02170.02160.03720.00210.010.06260.0391-0.02060.01180.0884-0.00520.00710.0763-0.00730.036-8.2566-5.013366.1113
61.11730.7701-0.46430.8867-0.21960.53080.1323-0.2937-0.03340.2921-0.124-0.010.00790.1776-0.00830.1828-0.006-0.0130.1686-0.01160.01814.5777-1.061182.9024
70.64630.1444-0.14470.60370.06170.2434-0.02330.0049-0.04760.00320.00020.01320.0268-0.03440.02320.0931-0.00670.0050.0752-0.0010.03344.8157-5.001721.6518
80.98870.5985-0.24870.5208-0.05160.43180.15-0.2601-0.06810.148-0.1515-0.04930.01610.05430.00150.1473-0.0265-0.02250.13770.02530.008617.2162-0.316539.3617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 211
2X-RAY DIFFRACTION2A212 - 308
3X-RAY DIFFRACTION3B17 - 211
4X-RAY DIFFRACTION4B212 - 308
5X-RAY DIFFRACTION5C17 - 212
6X-RAY DIFFRACTION6C213 - 312
7X-RAY DIFFRACTION7D17 - 212
8X-RAY DIFFRACTION8D213 - 313

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