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- PDB-3fge: Crystal structure of putative flavin reductase with split barrel ... -

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Basic information

Entry
Database: PDB / ID: 3fge
TitleCrystal structure of putative flavin reductase with split barrel domain (YP_750721.1) from SHEWANELLA FRIGIDIMARINA NCIMB 400 at 1.74 A resolution
Componentsputative flavin reductase with split barrel domain
KeywordsOXIDOREDUCTASE / YP_750721.1 / putative flavin reductase with split barrel domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homology
Function and homology information


FMN binding / metal ion binding
Similarity search - Function
Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
Flavin_Reduct domain-containing protein
Similarity search - Component
Biological speciesShewanella frigidimarina NCIMB 400 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative flavin reductase with split barrel domain (YP_750721.1) from SHEWANELLA FRIGIDIMARINA NCIMB 400 at 1.74 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
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_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_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

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Assembly

Deposited unit
A: putative flavin reductase with split barrel domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0604
Polymers22,9181
Non-polymers1423
Water2,648147
1
A: putative flavin reductase with split barrel domain
hetero molecules

A: putative flavin reductase with split barrel domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1218
Polymers45,8362
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8460 Å2
ΔGint-77 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.351, 65.502, 96.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY INDICATES A DIMER IS A BIOLOGICALLY SIGNIFICANT OLIGIOMERIZATION STATE.

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Components

#1: Protein putative flavin reductase with split barrel domain


Mass: 22918.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina NCIMB 400 (bacteria)
Gene: Sfri_2037, YP_750721.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q082D2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) 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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2000M Ca(OAc)2, 20.0000% PEG-3000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 1.74→27.929 Å / Num. obs: 19361 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.592 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.74-1.793.20.5891.8431713460.58996.9
1.79-1.833.60.4642.6500613970.464100
1.83-1.893.70.3763.3486213320.37699.9
1.89-1.953.60.2914.3474313080.291100
1.95-2.013.70.2525.1472212720.252100
2.01-2.083.70.1916.9447912180.191100
2.08-2.163.70.178432011740.17100
2.16-2.253.70.1399.7419311440.139100
2.25-2.353.70.12810.9403210940.128100
2.35-2.463.70.11711.9390010620.117100
2.46-2.593.70.10113.936769980.101100
2.59-2.753.70.08515.535309600.085100
2.75-2.943.70.07518.632718910.07599.9
2.94-3.183.60.07321.129908260.073100
3.18-3.483.50.06824.627507780.068100
3.48-3.893.60.05327.625497120.053100
3.89-4.493.60.0482922326270.048100
4.49-5.53.50.04528.919285460.045100
5.5-7.783.50.05225.314684240.052100
7.78-27.933.10.054257902520.05497.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.74→27.929 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.646 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.116
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 PROTEIN ...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. UNEXPLAINED ELECTRON DENSITY NEAR THE SIDECHAIN OF CYS 123 WAS NOT MODELED. 5.CA IONs FROM CRYSTALLIZATION ARE MODELED INTO THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 988 5.1 %RANDOM
Rwork0.167 ---
obs0.169 19333 99.74 %-
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: 63.57 Å2 / Biso mean: 24.627 Å2 / Biso min: 8.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--1.45 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.74→27.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 6 147 1651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211605
X-RAY DIFFRACTIONr_bond_other_d0.0020.02996
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9372195
X-RAY DIFFRACTIONr_angle_other_deg1.01632455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3225.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44915245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.83154
X-RAY DIFFRACTIONr_chiral_restr0.0590.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021868
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02316
X-RAY DIFFRACTIONr_nbd_refined0.2140.3335
X-RAY DIFFRACTIONr_nbd_other0.1810.31049
X-RAY DIFFRACTIONr_nbtor_refined0.1770.5813
X-RAY DIFFRACTIONr_nbtor_other0.090.5816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.5213
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1040.52
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.361
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.529
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1390.51
X-RAY DIFFRACTIONr_mcbond_it2.31531061
X-RAY DIFFRACTIONr_mcbond_other0.6813417
X-RAY DIFFRACTIONr_mcangle_it3.26151662
X-RAY DIFFRACTIONr_scbond_it4.9988617
X-RAY DIFFRACTIONr_scangle_it6.56111533
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 85 -
Rwork0.23 1254 -
all-1339 -
obs--96.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.43760.2163-0.99820.1021-0.64624.15780.0024-0.09430.0403-0.06080.00510.20140.1804-0.3269-0.0074-0.0154-0.00370.0258-0.012-0.0003-0.003419.956616.648642.0219
21.07260.16850.55590.95170.28841.98680.0153-0.0019-0.08870.0191-0.0123-0.00740.0304-0.1658-0.003-0.0674-0.0077-0.0023-0.06350.015-0.037422.259916.531513.6479
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 24
2X-RAY DIFFRACTION2A25 - 195

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