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- PDB-3v76: The crystal structure of a flavoprotein from Sinorhizobium meliloti -

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Basic information

Entry
Database: PDB / ID: 3v76
TitleThe crystal structure of a flavoprotein from Sinorhizobium meliloti
ComponentsFlavoprotein
KeywordsFLAVOPROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


HI0933 insert domain-like / 3-Dehydro-bile acid delta(4,6)-reductase-like / HI0933-like insert domain superfamily / HI0933-like protein Rossmann domain / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Helicase, Ruva Protein; domain 3 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...HI0933 insert domain-like / 3-Dehydro-bile acid delta(4,6)-reductase-like / HI0933-like insert domain superfamily / HI0933-like protein Rossmann domain / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Helicase, Ruva Protein; domain 3 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Uncharacterized protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsZhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of a flavoprotein from Sinorhizobium meliloti
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2812
Polymers45,4931
Non-polymers7881
Water1,874104
1
A: Flavoprotein
hetero molecules

A: Flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5614
Polymers90,9862
Non-polymers1,5752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4920 Å2
ΔGint-29 kcal/mol
Surface area30590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.091, 101.091, 106.934
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21A-448-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Flavoprotein


Mass: 45493.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R00707, SMc00763 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q92RY0
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.47 Å3/Da / Density % sol: 64.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5 M sodium formate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2011 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 21143 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 5.3 / Num. unique all: 2171 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GQF

2gqf


Resolution: 2.51→43.774 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 26.28 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1058 5.16 %RANDOM
Rwork0.1967 ---
obs0.1995 20523 93.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.53 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.4442 Å20 Å2-0 Å2
2--11.4442 Å20 Å2
3----22.8885 Å2
Refinement stepCycle: LAST / Resolution: 2.51→43.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 53 104 3091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133048
X-RAY DIFFRACTIONf_angle_d1.4314130
X-RAY DIFFRACTIONf_dihedral_angle_d20.1931135
X-RAY DIFFRACTIONf_chiral_restr0.088455
X-RAY DIFFRACTIONf_plane_restr0.01530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5099-2.62410.30311310.22422413X-RAY DIFFRACTION93
2.6241-2.76240.29181560.23142441X-RAY DIFFRACTION96
2.7624-2.93550.27971270.22572539X-RAY DIFFRACTION98
2.9355-3.16210.28811450.22432538X-RAY DIFFRACTION99
3.1621-3.48020.26731360.20062559X-RAY DIFFRACTION98
3.4802-3.98350.249910.19331583X-RAY DIFFRACTION61
3.9835-5.01760.20211320.1522643X-RAY DIFFRACTION100
5.0176-43.78030.21721400.18692749X-RAY DIFFRACTION100

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