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- PDB-4e6p: Crystal structure of a probable sorbitol dehydrogenase (Target PS... -

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Basic information

Entry
Database: PDB / ID: 4e6p
TitleCrystal structure of a probable sorbitol dehydrogenase (Target PSI-012078) from Sinorhizobium meliloti 1021
ComponentsProbable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
KeywordsOXIDOREDUCTASE / NAD(P)-binding / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium (NYSGRC)
Function / homology
Function and homology information


L-iditol 2-dehydrogenase / L-iditol 2-dehydrogenase (NAD+) activity / quinone binding / fatty acid biosynthetic process
Similarity search - Function
PKS_KR / 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
Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.096 Å
AuthorsKumar, P.R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a probable sorbitol dehydrogenase from Sinorhizobium meliloti 1021
Authors: Kumar, P.R. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Matikainen, B. / Seidel, R. / Toro, R. / ...Authors: Kumar, P.R. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Matikainen, B. / Seidel, R. / Toro, R. / Zencheck, W. / Almo, S.C.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
B: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
C: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
D: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,59725
Polymers111,4504
Non-polymers1,14721
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17110 Å2
ΔGint-66 kcal/mol
Surface area34010 Å2
MethodPISA
2
A: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
D: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,20511
Polymers55,7252
Non-polymers4809
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-23 kcal/mol
Surface area20610 Å2
MethodPISA
3
A: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
B: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26712
Polymers55,7252
Non-polymers54310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-16 kcal/mol
Surface area20380 Å2
MethodPISA
4
B: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
C: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,39114
Polymers55,7252
Non-polymers66712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-13 kcal/mol
Surface area21010 Å2
MethodPISA
5
C: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
D: Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,32913
Polymers55,7252
Non-polymers60511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-12 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.190, 90.407, 87.228
Angle α, β, γ (deg.)90.000, 118.080, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is probably a tetramer

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Components

#1: Protein
Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)


Mass: 27862.400 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: smoS, R02441, SMc01500 / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92N06, L-iditol 2-dehydrogenase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: THE CRYSTAL WAS SOAKED WITH 5mM NAD BEFORE FREEZING. Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Potassium Chloride, 20% PEG 3350 - MCSG1 #89), Cryoprotection ...Details: THE CRYSTAL WAS SOAKED WITH 5mM NAD BEFORE FREEZING. Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Potassium Chloride, 20% PEG 3350 - MCSG1 #89), Cryoprotection (Ethylene glycol), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2011 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 65989 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.25 Å2 / Rmerge(I) obs: 0.058 / Χ2: 0.855 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.145.90.18231140.885193.5
2.14-2.185.90.15831160.861194.3
2.18-2.225.90.1531910.884195.6
2.22-2.265.90.14332340.96196.9
2.26-2.3160.12332590.856197.8
2.31-2.376.10.11532810.849198.6
2.37-2.426.30.10833130.854199.2
2.42-2.496.40.10933050.89199.3
2.49-2.566.60.10333270.93199.6
2.56-2.656.80.09932900.931199.6
2.65-2.746.90.08933610.995199.6
2.74-2.857.10.08533041.011199.8
2.85-2.987.20.07533441.015199.8
2.98-3.147.40.06733451.01199.7
3.14-3.337.50.05733460.895199.9
3.33-3.597.60.04733590.8091100
3.59-3.957.60.04233580.8031100
3.95-4.527.60.03533440.677199.9
4.52-5.77.60.03233940.5571100
5.7-507.40.03134040.542198.8

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-55.506-43.71-26.343S201
2-47.66-29.007-12.514S200.96
3-48.079-41.674-42.422S200.96
4-67.983-51.4323.454S200.95
5-37.949-43.654-15.784S200.91
6-76.484-36.681-19.811S200.88
7-62.614-25.856-16.036S200.87
8-71.393-36.215-5.345S200.87
9-47.29-28.993-33.107S200.87
10-30.372-31.089-10.241S200.86
11-60.403-46.932-12.232S200.85
12-79.978-21.381-17.593S200.85
13-64.339-36.2151.793S200.85
14-41.808-34.516-27.881S200.85
15-39.287-38.179-23.614S200.85
16-74.082-36.614-10.276S200.84
17-84.642-28.044-28.311S200.68
18-46.459-14.184-24.324S200.66
19-74.828-53.028-23.121S200.62
20-44.854-58.552-21.548S200.59
21-60.926-19.9421.899S200.59
22-61.464-44.80213.125S200.56
23-28.323-43.567-4.819S200.51
24-51.855-29.094-47.176S200.43
25-28.266-36.579-32.302S200.26
26-85.084-36.486-1.014S200.22
27-90.953-41.163-27.219S200.22
28-29.689-45.873-31.964S200.19
29-96.549-31.1470.368S200.18
30-92.095-36.359-21.257S200.17
31-67.339-53.9956.068S200.11
32-81.512-26.369-28.922S200.1
33-99.797-36.75115.901S200.09
34-61.155-47.258-16.05S200.09
35-44.472-29.741-30.875S200.01

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.096→29.302 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8805 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.09 / Stereochemistry target values: ML
Details: PARTIAL NAD DENSITY IS OBSERVED IN ALL 4 MONOMERS AT THE SAME POSITION. ALTHOUGH THIS PARTIAL DENSITY IS SEEN IT IS NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 3324 5.04 %random
Rwork0.1611 ---
obs0.1633 65912 98.49 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.346 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 85.71 Å2 / Biso mean: 25.5247 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.4366 Å2-0 Å20.838 Å2
2--0.0706 Å2-0 Å2
3---0.366 Å2
Refinement stepCycle: LAST / Resolution: 2.096→29.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7624 0 72 531 8227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097832
X-RAY DIFFRACTIONf_angle_d1.01210593
X-RAY DIFFRACTIONf_chiral_restr0.071203
X-RAY DIFFRACTIONf_plane_restr0.0031392
X-RAY DIFFRACTIONf_dihedral_angle_d12.5942824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.096-2.12590.20181140.1492400251491
2.1259-2.15770.22261420.14452467260994
2.1577-2.19140.18741390.13942497263695
2.1914-2.22730.19071350.14562527266296
2.2273-2.26570.23081420.15172548269097
2.2657-2.30680.21261260.15372615274198
2.3068-2.35120.22811350.15252585272099
2.3512-2.39920.21041300.14492621275199
2.3992-2.45130.20371470.1512626277399
2.4513-2.50830.20361390.15892637277699
2.5083-2.5710.2321460.161926202766100
2.571-2.64050.22561370.165625972734100
2.6405-2.71810.20781350.155226512786100
2.7181-2.80580.23731560.17426162772100
2.8058-2.9060.26421410.167626412782100
2.906-3.02220.20391430.16532642278599
3.0222-3.15960.20021450.157526092754100
3.1596-3.3260.18171310.159926742805100
3.326-3.5340.20741150.1626522767100
3.534-3.80640.21011530.15126762829100
3.8064-4.18840.17751430.159226632806100
4.1884-4.79220.18411520.150326232775100
4.7922-6.0290.22171360.190226872823100
6.029-29.30450.1991420.18892714285699
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)
12.06920.0375-0.49882.05470.53532.3275-0.04430.65420.0582-0.510.0281-0.1451-0.028-0.0293-0.00340.2599-0.01120.06870.3126-0.00120.112568.13083.633-13.3793
22.0394-1.1293-0.01812.06250.08730.9930.00970.199-0.0822-0.2470.02030.00860.02320.0095-0.03420.1366-0.03350.0010.1375-0.00370.07356.41873.593-0.4052
33.9479-1.65751.94810.9016-1.13191.4411-0.02310.34110.467-0.15820.03290.015-0.10560.0430.02920.2242-0.003-0.01240.15510.10860.237255.092427.274-2.3081
42.0738-1.34260.13494.8842-0.57411.3835-0.0220.16390.2304-0.20490.0103-0.2085-0.11380.04980.02080.101-0.0210.00590.1074-0.01320.086769.12939.65645.6143
52.61220.0617-0.48331.85690.38882.1768-0.09980.1587-0.2073-0.0415-0.05330.30950.1538-0.19050.09310.0749-0.0192-0.0250.123-0.03570.201325.38610.930311.5988
61.4227-0.8593-0.20292.25070.43570.67890.020.1186-0.0907-0.1623-0.03740.2171-0.0254-0.09350.02680.1027-0.021-0.03360.10810.00670.08541.68874.44637.5051
71.1627-0.5854-1.8452.71382.58694.0351-0.01170.1333-0.50910.20760.03370.18240.9993-0.09870.1480.48740.016-0.11370.1422-0.04970.322748.664-16.284217.8719
82.5126-1.10220.47594.6989-0.65582.0107-0.04560.0036-0.12930.13020.05540.12450.13490.0019-0.00960.107-0.009-0.0140.1221-0.01640.079540.83715.943522.5966
92.4268-0.2101-0.312.17760.02012.22910.0587-0.28290.28990.31390.02810.1811-0.08980.0037-0.05090.1617-0.00830.0550.128-0.03340.124544.355116.625546.0308
101.3591.0568-0.73562.1882-0.58661.06160.0316-0.11570.02650.1636-0.01440.0204-0.03670.0124-0.01080.10510.0188-0.0160.0932-0.01350.070756.871113.38734.1065
114.50411.68230.52673.11540.64910.1396-0.2193-0.25430.8263-0.1452-0.01080.2307-0.3927-0.0590.11030.3607-0.0015-0.07780.1462-0.04320.28751.375333.944122.9909
121.570.2072-0.15785.1373-2.3952.3048-0.04330.03250.0431-0.01350.08310.1329-0.0233-0.0652-0.03950.0992-0.0049-0.03170.1295-0.02840.112843.508911.650526.8581
132.5688-0.0373-0.75091.46880.46111.8326-0.0614-0.1684-0.03720.14390.0283-0.30830.08080.35740.05330.0242-0.0191-0.00350.1477-0.01840.185388.299713.71122.9449
141.28190.6519-0.36162.0021-0.76571.29310.0124-0.05130.01280.0253-0.0324-0.2213-0.00660.12050.02890.07740.0178-0.01750.0986-0.01610.113171.159113.999326.0105
151.0277-0.6489-0.75951.3185-1.27625.4644-0.1343-0.1019-0.2110.1297-0.0004-0.11750.4410.2920.10810.1980.0491-0.01890.1150.02570.197571.6322-9.572128.0035
161.65080.5587-0.21256.3042-1.63321.7094-0.0770.0683-0.1714-0.1181-0.0507-0.21940.17960.12760.12330.12840.00170.01280.1104-0.02840.083272.68787.882212.0759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:90)A2 - 90
2X-RAY DIFFRACTION2chain 'A' and (resseq 91:185)A91 - 185
3X-RAY DIFFRACTION3chain 'A' and (resseq 186:222)A186 - 222
4X-RAY DIFFRACTION4chain 'A' and (resseq 223:257)A223 - 257
5X-RAY DIFFRACTION5chain 'B' and (resseq 2:90)B2 - 90
6X-RAY DIFFRACTION6chain 'B' and (resseq 91:185)B91 - 185
7X-RAY DIFFRACTION7chain 'B' and (resseq 186:222)B186 - 222
8X-RAY DIFFRACTION8chain 'B' and (resseq 223:257)B223 - 257
9X-RAY DIFFRACTION9chain 'C' and (resseq 2:90)C2 - 90
10X-RAY DIFFRACTION10chain 'C' and (resseq 91:185)C91 - 185
11X-RAY DIFFRACTION11chain 'C' and (resseq 186:222)C186 - 222
12X-RAY DIFFRACTION12chain 'C' and (resseq 223:257)C223 - 257
13X-RAY DIFFRACTION13chain 'D' and (resseq 2:90)D2 - 90
14X-RAY DIFFRACTION14chain 'D' and (resseq 91:185)D91 - 185
15X-RAY DIFFRACTION15chain 'D' and (resseq 186:222)D186 - 222
16X-RAY DIFFRACTION16chain 'D' and (resseq 223:257)D223 - 257

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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