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- PDB-3klb: Crystal structure of Putative Flavoprotein in Complex with FMN (Y... -

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Entry
Database: PDB / ID: 3klb
TitleCrystal structure of Putative Flavoprotein in Complex with FMN (YP_213683.1) from Bacteroides fragilis NCTC 9343 at 1.75 A resolution
ComponentsPutative Flavoprotein
KeywordsFLAVOPROTEIN / Putative Flavoprotein in Complex with FMN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Flavodoxin / Flavodoxin domain / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin-like domain-containing protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Flavoprotein in Complex with FMN (YP_213683.1) from Bacteroides fragilis NCTC 9343 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / software ...pdbx_struct_conn_angle / software / struct_conn / struct_conn_type
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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 Flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,58315
Polymers18,2991
Non-polymers1,28414
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.764, 96.764, 47.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-163-

NA

21A-195-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative Flavoprotein /


Mass: 18298.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: ATCC 25285 / NCTC 9343 / Gene: BF4115 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5L808

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Non-polymers , 5 types, 189 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT (1-161) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-161) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.0000% Glycerol, 1.2600M sodium citrate, 0.1M HEPES pH 7.5, Additive: 0.001 M FMN, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97939,0.97927
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979391
30.979271
ReflectionResolution: 1.75→27.832 Å / Num. obs: 23388 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.346 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.75-1.810.7321.9147993959194.2
1.81-1.890.5172.7182694815199.7
1.89-1.970.3523.9154974069199.7
1.97-2.070.2395.8161814237199.9
2.07-2.20.1668.4168644403199.7
2.2-2.370.11911.3168114384199.6
2.37-2.610.09314.5170814430199.8
2.61-2.990.05921.7171214430199.8
2.99-3.760.02641.6168604355199.7
3.76-27.8320.01959.9171144420199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→27.832 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.281 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.087
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). A MODIFIED FMN RESTRAINTS DICTIONARY WAS USED DURING THE REFINEMENT TO ALLOW BENDING OF THE FMN RING ALONG THE N5-N10 VIRTUAL AXIS. THIS RESULTS IN AN IMPROVED FIT BETWEEN THE FMN COORDINATE MODEL AND ELECTRON DENSITY. (5). SODIUM ION (NA) AND GLYCEROL (GOL) MOLECULES FROM CRYSTALLIZATION, AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO CONDITION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1196 5.1 %RANDOM
Rwork0.148 ---
obs0.15 23346 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 75.13 Å2 / Biso mean: 29.843 Å2 / Biso min: 15.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2---0.94 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 84 175 1517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221483
X-RAY DIFFRACTIONr_bond_other_d0.0010.021016
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9982015
X-RAY DIFFRACTIONr_angle_other_deg0.96132474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97423.79358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38815228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.835157
X-RAY DIFFRACTIONr_chiral_restr0.1010.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021652
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02302
X-RAY DIFFRACTIONr_nbd_refined0.2170.2281
X-RAY DIFFRACTIONr_nbd_other0.2010.21037
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2738
X-RAY DIFFRACTIONr_nbtor_other0.0830.2739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2136
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3170.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.212
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0860.22
X-RAY DIFFRACTIONr_mcbond_it1.7223878
X-RAY DIFFRACTIONr_mcbond_other0.5343351
X-RAY DIFFRACTIONr_mcangle_it2.80351432
X-RAY DIFFRACTIONr_scbond_it4.3278642
X-RAY DIFFRACTIONr_scangle_it5.99711583
LS refinement shellResolution: 1.752→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 77 -
Rwork0.205 1597 -
all-1674 -
obs--98.99 %
Refinement TLS params.Method: refined / Origin x: 31.3526 Å / Origin y: 10.2525 Å / Origin z: 29.4288 Å
111213212223313233
T-0.0493 Å20.0069 Å20.0042 Å2--0.038 Å20.0046 Å2---0.0601 Å2
L1.2386 °2-0.0659 °20.0748 °2-1.2571 °20.3734 °2--0.6885 °2
S-0.0074 Å °-0.0201 Å °0.0202 Å °-0.0269 Å °-0.0022 Å °-0.0244 Å °-0.0316 Å °0.0109 Å °0.0096 Å °

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