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- PDB-3fvw: Crystal structure of the Q8DWD8_STRMU protein from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 3fvw
TitleCrystal structure of the Q8DWD8_STRMU protein from Streptococcus mutans. Northeast Structural Genomics Consortium target SmR99.
ComponentsPutative NAD(P)H-dependent FMN reductase
Keywordsstructural genomics / unknown function / Q8DWD8_STRMU / putative NAD(P)H-dependent FMN reductase / SmR99 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyNADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / oxidoreductase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FMN_red domain-containing protein
Function and homology information
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Belote, R.L. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. / Hunt, J.F. ...Vorobiev, S.M. / Abashidze, M. / Belote, R.L. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Q8DWD8_STRMU protein from Streptococcus mutans.
Authors: Vorobiev, S.M. / Abashidze, M. / Belote, R.L. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative NAD(P)H-dependent FMN reductase
B: Putative NAD(P)H-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)43,0162
Polymers43,0162
Non-polymers00
Water2,018112
1
A: Putative NAD(P)H-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)21,5081
Polymers21,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative NAD(P)H-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)21,5081
Polymers21,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.297, 99.297, 90.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsauthors claim that the biological unit is monomer according to aggregation screening

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Components

#1: Protein Putative NAD(P)H-dependent FMN reductase


Mass: 21507.816 Da / Num. of mol.: 2 / Mutation: V182I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: ATCC 700610/UA159/Serotype c / Gene: SMU_125 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q8DWD8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 18-20% PEG 3350, 0.2M DL-Malic acid, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97862, 0.97922, 0.91837,
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 10, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978621
20.979221
30.918371
ReflectionResolution: 2.3→50 Å / Num. all: 44160 / Num. obs: 44160 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 15.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2.03 / Num. unique all: 4404 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
Web-Icedata collection
SHELXD/Emodel building
RESOLVEmodel building
CNS1.2 (using xtal_twin utilities)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXD/Ephasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Crystal has partial merohedral twinning; twinning operator= -h,-k,l twinning fraction= 0.25 (detected by CNS 1.2 detect_twinning.inp)
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 1970 -RANDOM
Rwork0.188 ---
all-44195 --
obs-42245 95.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.062 Å20 Å20 Å2
2--8.062 Å20 Å2
3----16.124 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2789 0 0 112 2901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007315
X-RAY DIFFRACTIONc_angle_d1.30511
X-RAY DIFFRACTIONc_dihedral_angle_d23.88483
X-RAY DIFFRACTIONc_improper_angle_d0.83797
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.3074 177 -
Rwork0.3227 --
obs-3799 86.14 %

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