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- PDB-3in6: Crystal structure of a fmn-binding protein (swol_0183) from syntr... -

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Basic information

Entry
Database: PDB / ID: 3in6
TitleCrystal structure of a fmn-binding protein (swol_0183) from syntrophomonas wolfei subsp. wolfei at 2.12 A resolution
ComponentsFMN-binding protein
KeywordsFLAVOPROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Single helix bin / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Uncharacterized protein
Similarity search - Component
Biological speciesSyntrophomonas wolfei subsp. wolfei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of FMN-binding protein (YP_752906.1) from Syntrophomonas wolfei str. Goettingen at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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 / 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: FMN-binding protein
B: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4005
Polymers34,3692
Non-polymers1,0313
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-51 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.108, 103.108, 59.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A5 - 146
2116B5 - 146
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein FMN-binding protein


Mass: 17184.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophomonas wolfei subsp. wolfei (bacteria)
Strain: Goettingen / Gene: Swol_0183, YP_752906.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q0B0G9
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.29
Details: 30.5000% 2-methyl-2,4-pentanediol, 0.1M sodium acetate pH 4.29, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97936,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 20, 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
20.979361
30.979221
ReflectionResolution: 2.12→28.712 Å / Num. obs: 18788 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.12 % / Biso Wilson estimate: 35.044 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.01
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.12-2.20.5542.5138003674199.5
2.2-2.280.4613120443141199.1
2.28-2.390.3853.6142133692198.9
2.39-2.510.2894.7127093303199.4
2.51-2.670.26.7135923530199.6
2.67-2.880.1429.4136483537199.5
2.88-3.160.08514.7131413396199.8
3.16-3.620.04625.4136413533199.7
3.62-4.550.02739.5134293477199.8
4.55-28.7120.0249.8136233538199.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.12→28.712 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 13.723 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.202
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.ENDOGENOUS FLAVIN MONONUCLEOTIDE(FMN) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON CLEAR ELECTRON DENSITY. 5.2,4-METHANEPENTANEDIOL (MPD) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 958 5.1 %RANDOM
Rwork0.219 ---
obs0.221 18752 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.15 Å2 / Biso mean: 29.909 Å2 / Biso min: 2.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.9 Å20 Å20 Å2
2---2.9 Å20 Å2
3---5.81 Å2
Refinement stepCycle: LAST / Resolution: 2.12→28.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 70 41 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222397
X-RAY DIFFRACTIONr_bond_other_d0.0010.021572
X-RAY DIFFRACTIONr_angle_refined_deg1.4312.0173254
X-RAY DIFFRACTIONr_angle_other_deg0.84233853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4835294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.96124.43397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28915430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4271515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02457
X-RAY DIFFRACTIONr_mcbond_it1.30131459
X-RAY DIFFRACTIONr_mcbond_other0.3423597
X-RAY DIFFRACTIONr_mcangle_it2.35952362
X-RAY DIFFRACTIONr_scbond_it4.4438938
X-RAY DIFFRACTIONr_scangle_it6.17411891
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1810 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.715
LOOSE THERMAL3.0810
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 66 -
Rwork0.305 1282 -
all-1348 -
obs--99.56 %
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)
13.4832-1.63850.94293.4761-0.50050.2637-0.141-0.4762-0.0550.20510.1570.1113-0.0188-0.1457-0.0160.14210.01790.02640.15930.00270.0067-14.1294-37.472212.1492
23.525-2.3592-0.58953.8445-0.01431.0539-0.3279-0.40830.93210.4570.2303-0.9047-0.10660.05420.09770.10660.0431-0.15110.1096-0.1170.3448-11.2647-15.022814.4023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 146
2X-RAY DIFFRACTION2B0 - 146

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