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- PDB-3nx4: Crystal structure of the yhdH oxidoreductase from Salmonella ente... -

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Basic information

Entry
Database: PDB / ID: 3nx4
TitleCrystal structure of the yhdH oxidoreductase from Salmonella enterica in complex with NADP
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / PSI / Protein Structure Initiative
Function / homology
Function and homology information


acryloyl-CoA reductase (NADPH) activity / nucleotide binding
Similarity search - Function
Acrylyl-CoA reductase AcuI / : / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...Acrylyl-CoA reductase AcuI / : / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Peterson, S. / Onopriyenko, O. / Skarina, T. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of the yhdH oxidoreductase from Salmonella enterica in complex with NADP
Authors: Anderson, S.M. / Wawrzak, Z. / Peterson, S. / Onopriyenko, O. / Skarina, T. / Anderson, W.F. / Savchenko, A.
History
DepositionJul 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0884
Polymers69,6012
Non-polymers1,4872
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-21 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.218, 122.364, 64.912
Angle α, β, γ (deg.)90.0, 121.1, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative oxidoreductase


Mass: 34800.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: yhdH, STM3376 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q7CPM2
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 200mM Ammonium Citrate, 10mM NADP, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2010 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 54356 / Num. obs: 51747 / % possible obs: 95.2 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.5 / Redundancy: 9.4 % / Biso Wilson estimate: 26.42 Å2 / Rmerge(I) obs: 0.101 / Χ2: 1.002 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.976.50.5462.5645670.98483.8
1.97-2.057.10.3934.1747661.01888.3
2.05-2.147.60.3145.7849571.06292
2.14-2.258.30.2557.8951561.01195
2.25-2.399.40.2381053070.98997.7
2.39-2.5810.50.21412.8353610.98898.5
2.58-2.8410.90.15517.485353198.8
2.84-3.25110.1119.2553860.98299.1
3.25-4.0910.90.07822.0254221.01799.3
4.09-5010.50.07123.1154720.98999.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.042 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8373 / SU ML: 0.22 / σ(F): 1.44 / σ(I): 2.56 / Phase error: 23.08 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 1994 3.87 %random
Rwork0.1547 ---
obs0.1561 51577 95.11 %-
all-54229 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.308 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso max: 258.92 Å2 / Biso mean: 46.0728 Å2 / Biso min: 15.89 Å2
Baniso -1Baniso -2Baniso -3
1-4.6038 Å2-0 Å218.6204 Å2
2---6.5856 Å2-0 Å2
3---1.9818 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 96 404 5338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075047
X-RAY DIFFRACTIONf_angle_d1.126872
X-RAY DIFFRACTIONf_chiral_restr0.073784
X-RAY DIFFRACTIONf_plane_restr0.005879
X-RAY DIFFRACTIONf_dihedral_angle_d15.531832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.96790.29672270.266343554530453883.6
1.9679-2.04670.26812370.224945554739474588.1
2.0467-2.13980.23142480.189147694961496491.9
2.1398-2.25260.21362560.166349185115512294.8
2.2526-2.39370.20012650.159850945299530497.6
2.3937-2.57850.20972680.1651495356536198.4
2.5785-2.83790.19662670.154651295335534298.7
2.8379-3.24840.18892680.149551605368536499.1
3.2484-4.09180.15282710.131352055413541599.4
4.0918-37.04930.17522730.142252495461546399.5
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)
10.2193-0.01190.06350.33030.07640.84860.4290.44920.1069-0.5605-0.3714-0.0397-0.2287-0.7127-0.00780.58810.28840.00240.55660.06570.313321.753150.6581-10.522
20.5836-0.08740.18580.69540.32950.3180.40140.17050.3959-0.091-0.1689-0.2332-0.2388-0.36020.00710.41930.23470.05640.43890.11710.285220.769754.8867-4.1814
30.9322-0.1891-0.75480.8112-0.19181.47330.10150.0710.1259-0.1098-0.0492-0.1744-0.0615-0.1774-0.00090.20320.05580.00290.17870.0160.209132.116740.64645.8148
40.8442-0.3019-0.80581.2227-0.39411.38030.10520.15760.0229-0.254-0.1041-0.11980.0755-0.32790.00570.2490.0352-0.0150.241-0.00910.19329.03534.16585.7172
52.1125-0.1434-1.1280.15360.33311.057-0.50320.1134-1.23970.152-0.1311-0.00530.9578-0.1772-0.14930.6533-0.17130.23420.2302-0.1790.641414.4517-0.505534.1869
60.2575-0.010.10860.05140.0070.1086-0.2850.0236-0.6782-0.0072-0.102-0.11070.62460.165500.5016-0.00570.17070.2644-0.04890.51719.79613.810337.5596
71.4527-0.1032-0.55910.5339-1.08622.4288-0.11450.1512-0.13110.20380.12610.05130.1732-0.4763-0.00210.1483-0.06590.00120.2709-0.04560.217410.11420.997931.2158
81.00440.19-1.33380.4092-0.27671.9325-0.06090.3084-0.06950.03030.03780.07480.1321-0.5447-00.1798-0.0906-0.03330.3557-0.03670.21949.643321.50524.1639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:54)A1 - 54
2X-RAY DIFFRACTION2(chain A and resid 55:73)A55 - 73
3X-RAY DIFFRACTION3(chain A and resid 74:205)A74 - 205
4X-RAY DIFFRACTION4(chain A and resid 206:324)A206 - 324
5X-RAY DIFFRACTION5(chain B and resid 1:54)B1 - 54
6X-RAY DIFFRACTION6(chain B and resid 55:73)B55 - 73
7X-RAY DIFFRACTION7(chain B and resid 74:205)B74 - 205
8X-RAY DIFFRACTION8(chain B and resid 206:324)B206 - 324

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