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- PDB-3ec7: Crystal Structure of Putative Dehydrogenase from Salmonella typhi... -

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Basic information

Entry
Database: PDB / ID: 3ec7
TitleCrystal Structure of Putative Dehydrogenase from Salmonella typhimurium LT2
ComponentsPutative Dehydrogenase
KeywordsOXIDOREDUCTASE / alpha-beta / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / unknown function
Function / homology
Function and homology information


inositol 2-dehydrogenase / inositol 2-dehydrogenase (NAD+) activity / inositol catabolic process / nucleotide binding
Similarity search - Function
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase / : / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase / : / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Inositol 2-dehydrogenase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsKim, Y. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Dehydrogenase from Salmonella typhimurium LT2
Authors: Kim, Y. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Putative Dehydrogenase
B: Putative Dehydrogenase
C: Putative Dehydrogenase
D: Putative Dehydrogenase
E: Putative Dehydrogenase
F: Putative Dehydrogenase
G: Putative Dehydrogenase
H: Putative Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,01833
Polymers321,2968
Non-polymers7,72225
Water37,2732069
1
A: Putative Dehydrogenase
B: Putative Dehydrogenase
C: Putative Dehydrogenase
D: Putative Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,47616
Polymers160,6484
Non-polymers3,82812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19830 Å2
ΔGint-44 kcal/mol
Surface area47920 Å2
MethodPISA
2
A: Putative Dehydrogenase
B: Putative Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2478
Polymers80,3242
Non-polymers1,9246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-16 kcal/mol
Surface area27350 Å2
MethodPISA
3
C: Putative Dehydrogenase
D: Putative Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2298
Polymers80,3242
Non-polymers1,9056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-18 kcal/mol
Surface area27430 Å2
MethodPISA
4
E: Putative Dehydrogenase
F: Putative Dehydrogenase
G: Putative Dehydrogenase
H: Putative Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,54217
Polymers160,6484
Non-polymers3,89413
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-35 kcal/mol
Surface area47720 Å2
MethodPISA
5
E: Putative Dehydrogenase
F: Putative Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2518
Polymers80,3242
Non-polymers1,9286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-12 kcal/mol
Surface area27390 Å2
MethodPISA
6
G: Putative Dehydrogenase
H: Putative Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2919
Polymers80,3242
Non-polymers1,9677
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-18 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.001, 98.981, 105.790
Angle α, β, γ (deg.)88.05, 81.78, 89.92
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Putative Dehydrogenase


Mass: 40161.938 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: N-terminal 6-His-tag / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BM21DE3 / References: UniProt: Q8ZK57

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Non-polymers , 6 types, 2094 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2069 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.2M K Acetate, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→47 Å / Num. all: 174149 / Num. obs: 174149 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.7
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.33 / % possible all: 96.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0053 & phenix.refinerefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.715 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.192
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23066 8685 5 %RANDOM
Rwork0.17594 ---
obs0.17869 165089 98.07 %-
all-165089 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å2-1 Å2-1.61 Å2
2--0.1 Å2-0.08 Å2
3---2.84 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20908 0 502 2069 23479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02222041
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.97630035
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0252718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55924.924993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48153615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.06515104
X-RAY DIFFRACTIONr_chiral_restr0.1050.23402
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116544
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_it0.7021.513480
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.208221833
X-RAY DIFFRACTIONr_scbond_it2.3638561
X-RAY DIFFRACTIONr_scangle_it3.5374.58202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.147→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 635 -
Rwork0.206 11756 -
obs--96.65 %
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)
10.602-0.0166-0.10840.80770.11120.4490.05190.1645-0.0598-0.2201-0.0522-0.00420.0216-0.02250.00040.07380.0314-0.0050.058-0.01150.010736.2939.381.167
20.59470.0351-0.04471.1712-0.05190.43710.0438-0.232-0.06730.4156-0.0506-0.10070.04320.03290.00680.1626-0.0277-0.03990.11620.0340.016638.55410.16243.937
30.8422-0.2050.17870.89930.03350.4912-0.0681-0.3410.10370.33380.03930.0914-0.0424-0.12310.02890.13290.01740.04160.1497-0.04820.0517.23941.59544.329
40.841-0.21210.29720.776-0.03850.57920.0740.24450.1362-0.24-0.12140.0416-0.03740.06180.04750.08130.0423-0.0050.0770.03390.058718.91343.2140.762
50.92140.3018-0.20890.768-0.06370.32640.1194-0.2391-0.08170.2098-0.13680.00480.02620.05140.01730.0718-0.0418-0.00890.07380.00990.024359.67859.12931.948
60.88110.3145-0.05410.76450.07360.3694-0.08850.3674-0.0554-0.30740.07570.05220.0331-0.03930.01290.1391-0.0122-0.02630.1688-0.03590.024757.78659.612-10.763
70.99630.30750.21020.72630.05580.4768-0.1140.40090.1329-0.26880.0685-0.0701-0.05670.13380.04550.1068-0.02560.03290.17750.0670.064279.08290.875-11.048
80.97210.32810.33650.61120.1680.60860.1026-0.28450.16220.1967-0.1446-0.00290.016-0.06510.04210.0685-0.04660.0070.093-0.03650.072677.16892.68832.517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 336
2X-RAY DIFFRACTION2B2 - 336
3X-RAY DIFFRACTION3C2 - 336
4X-RAY DIFFRACTION4D1 - 336
5X-RAY DIFFRACTION5E1 - 336
6X-RAY DIFFRACTION6F2 - 336
7X-RAY DIFFRACTION7G2 - 336
8X-RAY DIFFRACTION8H1 - 336

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