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- PDB-4ipt: The crystal structure of a short-chain dehydrogenases/reductase (... -

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Basic information

Entry
Database: PDB / ID: 4ipt
TitleThe crystal structure of a short-chain dehydrogenases/reductase (ethylated) from Veillonella parvula DSM 2008
ComponentsNAD-dependent epimerase/dehydratase
KeywordsLYASE / ISOMERASE / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / NAD-dependent epimerase/dehydratase
Similarity search - Component
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.546 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a short-chain dehydrogenases/reductase (ethylated) from Veillonella parvula DSM 2008
Authors: Tan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.
History
DepositionJan 10, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 6, 2013ID: 3R14
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6398
Polymers25,0841
Non-polymers5557
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.681, 60.758, 68.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. It is predicted to be a monomer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-dependent epimerase/dehydratase / short-chain dehydrogenases/reductase


Mass: 25083.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_0111 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1BQI7

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Non-polymers , 6 types, 137 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M CACL2, 0.1M BIS-TRIS:HCL, 30% (V/V) PEG MME 550, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2010 / Details: mirror
RadiationMonochromator: SI 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.55→42 Å / Num. all: 31918 / Num. obs: 31918 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 45
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.546→41.315 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 1618 5.08 %
Rwork0.1866 --
obs0.1882 31850 98.47 %
all-31850 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.546→41.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 34 130 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061847
X-RAY DIFFRACTIONf_angle_d1.0382500
X-RAY DIFFRACTIONf_dihedral_angle_d16.198712
X-RAY DIFFRACTIONf_chiral_restr0.069277
X-RAY DIFFRACTIONf_plane_restr0.004318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5464-1.59190.3391320.25772460X-RAY DIFFRACTION97
1.5919-1.64330.30871240.24522511X-RAY DIFFRACTION100
1.6433-1.7020.26541270.23112530X-RAY DIFFRACTION100
1.702-1.77020.26811350.20142532X-RAY DIFFRACTION100
1.7702-1.85070.23391490.1932508X-RAY DIFFRACTION100
1.8507-1.94830.22881500.18462515X-RAY DIFFRACTION100
1.9483-2.07040.20691360.18282548X-RAY DIFFRACTION100
2.0704-2.23020.2391410.1792537X-RAY DIFFRACTION100
2.2302-2.45460.19311190.17952576X-RAY DIFFRACTION100
2.4546-2.80980.2261400.18172553X-RAY DIFFRACTION100
2.8098-3.53970.20141430.18482551X-RAY DIFFRACTION98
3.5397-41.32940.21541220.1832411X-RAY DIFFRACTION88
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)
15.76210.43350.22492.46190.07986.50870.1088-0.1674-0.27560.22330.0582-0.09580.35670.4045-0.12150.2290.0179-0.05920.2312-0.05260.182718.131349.456922.2256
23.93721.3701-0.42172.70371.22875.8530.5098-0.27390.00590.6531-0.1193-0.1803-0.56161.0882-0.4080.4191-0.0337-0.0380.4124-0.10640.266624.905255.701923.3223
34.81160.3413-0.3354.6331-0.4794.66180.008-0.15370.07360.39880.284-0.54-0.42771.4193-0.23120.2960.0107-0.08690.5289-0.17570.34829.51453.309817.6649
47.64760.7486-0.38372.58231.28072.2749-0.33060.2067-0.59810.21990.7231-0.03140.09860.7881-0.16080.26310.0512-0.01410.3578-0.13570.208120.85749.497811.7631
55.3775-6.83321.40739.8487-2.55285.15260.16840.82080.3563-0.54990.1121-0.8819-0.17541.0607-0.18650.2457-0.12480.02480.5792-0.14530.318825.431750.67133.3775
66.3029-3.26810.90344.2543-1.03123.2026-0.1090.4173-0.26130.00110.15650.02130.06330.2041-0.01890.2085-0.0223-0.01590.2252-0.05770.177512.167949.40176.6508
73.11242.50510.34535.08571.04754.253-0.33030.80111.6613-0.7910.28690.5577-1.1172-0.43850.18380.37380.0393-0.08810.31750.09860.4854-0.657664.50744.0432
87.0268-5.2172-0.36233.91840.60912.05150.08170.78330.2096-0.6865-0.1531-0.3261-0.5340.42560.06910.3645-0.1229-0.02510.38190.01660.200813.03356.3518-0.1042
94.1057-0.8632-0.35294.162.08544.2324-0.23130.16820.01580.13450.2714-0.07560.05320.30630.02570.1444-0.0239-0.00480.148-0.01080.13389.679250.34859.1108
104.9926-1.01521.45663.91810.63522.4111-0.1781-0.3375-0.04670.49580.00640.1966-0.0156-0.44360.13970.2371-0.0090.04850.2403-0.00680.17532.950850.475617.8995
113.57630.5427-1.13644.03390.39524.6969-0.24120.1361-0.57450.29670.2264-0.48610.95040.05570.04220.33390.00230.00170.1895-0.05140.28639.258840.130110.9689
123.0793-1.0702-2.27686.39160.06993.8635-0.1222-0.16510.36210.12340.19850.5402-0.51-0.6382-0.08140.28530.0880.03690.3235-0.0660.3817-5.480360.640115.8375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 81 )
5X-RAY DIFFRACTION5chain 'A' and (resid 82 through 94 )
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 113 )
7X-RAY DIFFRACTION7chain 'A' and (resid 114 through 125 )
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 141 )
9X-RAY DIFFRACTION9chain 'A' and (resid 142 through 155 )
10X-RAY DIFFRACTION10chain 'A' and (resid 156 through 190 )
11X-RAY DIFFRACTION11chain 'A' and (resid 191 through 206 )
12X-RAY DIFFRACTION12chain 'A' and (resid 207 through 218 )

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