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- PDB-3e18: CRYSTAL STRUCTURE OF NAD-BINDING PROTEIN FROM Listeria innocua -

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Basic information

Entry
Database: PDB / ID: 3.0E+18
TitleCRYSTAL STRUCTURE OF NAD-BINDING PROTEIN FROM Listeria innocua
Componentsoxidoreductase
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / NAD-BINDING / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / UNKNOWN FUNCTION / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
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 ...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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Lin2262 protein
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsPatskovsky, Y. / Ramagopal, U.A. / Toro, R. / Rutter, M. / Hu, S. / Groshong, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF NAD-BINDING PROTEIN FROM Listeria innocua
Authors: Patskovsky, Y. / Ramagopal, U.A. / Toro, R. / Rutter, M. / Hu, S. / Groshong, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: oxidoreductase
B: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,70617
Polymers79,3742
Non-polymers2,33215
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-42 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.083, 91.555, 96.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A4 - 258
2114B4 - 258
1124A293 - 357
2124B293 - 357

NCS ensembles :
ID
1
2
DetailsAuthors state that the biological assembly is likely homodimer, the ASU contains one homodimer composed of two monomers, A and B

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein oxidoreductase /


Mass: 39686.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin2262 / Production host: Escherichia coli (E. coli) / References: UniProt: Q929L3

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Non-polymers , 5 types, 433 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.54 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 100MM BIS-TRIS, PH 6.5, 25% PEG3350, 200MM MAGNESIUM CHLORIDE HEXAHYDRATE, 10% GLYCEROL, VAPOR DIFFUS SITTING DROP, TEMPERATURE 294K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 59448 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 6.2 % / Biso Wilson estimate: 28.45 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.816 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23656 1814 3.1 %RANDOM
Rwork0.1868 ---
obs0.18832 57400 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.157 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å20 Å20 Å2
2---2.46 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5335 0 151 418 5904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9717686
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82325.296253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28615940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3021516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024205
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.160.32490
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.53859
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.5701
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.334
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.539
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.30323513
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.30235526
X-RAY DIFFRACTIONr_scbond_it5.10232404
X-RAY DIFFRACTIONr_scangle_it7.3752152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11946medium positional0.371
2435medium positional0.351
11946medium thermal1.712.5
2435medium thermal1.662.5
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 115 -
Rwork0.265 4069 -
obs--97.55 %

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