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- PDB-3lcm: Crystal structure of Smu.1420 from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3lcm
TitleCrystal structure of Smu.1420 from Streptococcus mutans UA159
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / NADPH:quinone oxidoreductase / MdaB / Smu.1420
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) / NAD(P)H dehydrogenase (quinone) activity / nucleotide binding / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsWang, Z.X. / Su, X.-D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and biochemical characterization of MdaB from cariogenic Streptococcus mutans reveals an NADPH-specific quinone oxidoreductase
Authors: Wang, Z.X. / Li, L. / Dong, Y.H. / Su, X.-D.
History
DepositionJan 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,43012
Polymers91,3144
Non-polymers6,1168
Water6,612367
1
A: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7156
Polymers45,6572
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-15 kcal/mol
Surface area16780 Å2
MethodPISA
2
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7156
Polymers45,6572
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-15 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.601, 79.118, 106.281
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative oxidoreductase / Smu.1420


Mass: 22828.451 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.1420 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DTD1, EC: 1.6.99.2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M KCl, 0.05M HEPES pH7.5, 35% v/v Pentaerythritol propoxylate(5/4 PO/OH), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9796 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jan 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.425
ReflectionResolution: 1.799→50 Å / Num. all: 77829 / Num. obs: 73792 / % possible obs: 95.4 % / Redundancy: 3.5 % / Rsym value: 0.076
Reflection shellResolution: 1.799→1.83 Å / Redundancy: 3.2 % / Num. unique all: 3821 / Rsym value: 0.305 / % possible all: 92.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZX1

1zx1


Resolution: 1.799→29.019 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.729 / σ(F): 1.33 / Phase error: 33.88 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1877 2072 2.81 %
Rwork0.1603 71733 -
obs0.161 73733 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.14 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 64.34 Å2 / Biso mean: 21.748 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.697 Å20 Å2-5.601 Å2
2---1.334 Å2-0 Å2
3---3.031 Å2
Refinement stepCycle: LAST / Resolution: 1.799→29.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 265 367 6676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066503
X-RAY DIFFRACTIONf_angle_d1.0348919
X-RAY DIFFRACTIONf_dihedral_angle_d18.5662394
X-RAY DIFFRACTIONf_chiral_restr0.063981
X-RAY DIFFRACTIONf_plane_restr0.0051085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7993-1.83040.3269850.26743052X-RAY DIFFRACTION98
1.8304-1.86360.2706970.25073461X-RAY DIFFRACTION98
1.8636-1.89950.2538960.2353435X-RAY DIFFRACTION98
1.8995-1.93820.2595970.22733497X-RAY DIFFRACTION98
1.9382-1.98040.2486940.21393366X-RAY DIFFRACTION98
1.9804-2.02640.219970.20893491X-RAY DIFFRACTION98
2.0264-2.07710.2185950.19873423X-RAY DIFFRACTION98
2.0771-2.13320.2756970.19223460X-RAY DIFFRACTION98
2.1332-2.1960.2105980.19113526X-RAY DIFFRACTION98
2.196-2.26680.2195980.18623506X-RAY DIFFRACTION98
2.2668-2.34780.1911000.18073591X-RAY DIFFRACTION98
2.3478-2.44180.19271020.17623658X-RAY DIFFRACTION98
2.4418-2.55290.20381050.17453728X-RAY DIFFRACTION98
2.5529-2.68740.20921040.17133760X-RAY DIFFRACTION98
2.6874-2.85560.22021050.16963762X-RAY DIFFRACTION98
2.8556-3.07590.19441050.15563793X-RAY DIFFRACTION98
3.0759-3.3850.16191070.13953809X-RAY DIFFRACTION98
3.385-3.87380.14851060.11763792X-RAY DIFFRACTION98
3.8738-4.87680.12571060.10063808X-RAY DIFFRACTION98
4.8768-29.02240.15751060.15343815X-RAY DIFFRACTION98

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