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- PDB-3mcs: Crystal structure of Putative monooxygenase (FN1347) from FUSOBAC... -

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Basic information

Entry
Database: PDB / ID: 3mcs
TitleCrystal structure of Putative monooxygenase (FN1347) from FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM ATCC 25586 at 2.55 A resolution
ComponentsPutative monooxygenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Hypothetical cytosolic protein
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative monooxygenase (FN1347) from FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM ATCC 25586 at 2.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: 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 17, 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: Putative monooxygenase
B: Putative monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9624
Polymers50,8442
Non-polymers1182
Water73941
1
A: Putative monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4812
Polymers25,4221
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4812
Polymers25,4221
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.851, 66.243, 66.763
Angle α, β, γ (deg.)90.000, 98.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 217
2111B1 - 217
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein Putative monooxygenase /


Mass: 25422.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (bacteria)
Strain: ATCC 25586 / Gene: FN1347 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8RDZ4
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97925,0.97894
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979251
30.978941
ReflectionResolution: 2.55→29.607 Å / Num. obs: 14638 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.814 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.55-2.640.6541.351842693195.7
2.64-2.750.4571.957052946199
2.75-2.870.3332.653332740198.6
2.87-3.020.2413.555152838199
3.02-3.210.1685.154802819198.5
3.21-3.460.1017.955292834198.1
3.46-3.80.0711.353152727197.8
3.8-4.350.051555112817197.4
4.35-5.460.03619.154542783197.7
5.46-29.6070.0282256342875197.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.55→29.607 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 30.986 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.358
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONIN INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONIN 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. 3 .ACETATE (ACT) FROM THE CRYSTALLIZATION WAS MODELED INTO THE STRUCTURE 4.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ASN 90 ON BOTH THE A AND B CHAINS ARE FLAGGED AS MOLPROBITY RAMACHANDRAN OUTLIERS, AND IT IS LIKELY THAT THIS IS RELATED TO DISORDERED ELECTRON DENSITIES AT THIS RESIDUE.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1470 10.1 %RANDOM
Rwork0.212 ---
obs0.217 14626 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.26 Å2 / Biso mean: 44.749 Å2 / Biso min: 22.49 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å20 Å2-0.77 Å2
2---0.32 Å20 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 8 41 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223567
X-RAY DIFFRACTIONr_bond_other_d0.0020.022307
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9464848
X-RAY DIFFRACTIONr_angle_other_deg0.90635668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1085451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89625.806186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71115611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8021512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
X-RAY DIFFRACTIONr_mcbond_it0.95732199
X-RAY DIFFRACTIONr_mcbond_other0.4413892
X-RAY DIFFRACTIONr_mcangle_it1.6853545
X-RAY DIFFRACTIONr_scbond_it3.32181368
X-RAY DIFFRACTIONr_scangle_it4.763111296
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2696 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.030.05
TIGHT THERMAL0.090.5
LS refinement shellResolution: 2.552→2.618 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 107 -
Rwork0.336 943 -
all-1050 -
obs--97.95 %
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)
12.45520.1743-0.82181.99320.411.6208-0.0572-0.0183-0.04570.005-0.00070.15330.00630.01690.05790.02040.0083-0.01840.01-0.00210.058936.253236.182360.2242
21.57490.0410.40372.9063-0.17484.0783-0.1190.1754-0.0302-0.45490.00020.06250.0322-0.14910.11880.087-0.02690.00990.0506-0.03770.042440.254612.961137.1514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 217
2X-RAY DIFFRACTION2B0 - 217

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