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- PDB-3kkf: Crystal structure of Putative antibiotic biosynthesis monooxygena... -

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Basic information

Entry
Database: PDB / ID: 3kkf
TitleCrystal structure of Putative antibiotic biosynthesis monooxygenase (NP_810307.1) from Bacteriodes thetaiotaomicron VPI-5482 at 1.30 A resolution
ComponentsPutative antibiotic biosynthesis monooxygenase
KeywordsOXIDOREDUCTASE / Putative antibiotic biosynthesis monooxygenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
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 / Putative flavoredoxin
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative antibiotic biosynthesis monooxygenase (NP_810307.1) from Bacteriodes thetaiotaomicron VPI-5482 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_distant_solvent_atoms / pdbx_struct_conn_angle ...pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _struct_conn_type.id
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_conn_type / 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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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

Downloads & links

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Assembly

Deposited unit
A: Putative antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0737
Polymers12,3071
Non-polymers7666
Water2,504139
1
A: Putative antibiotic biosynthesis monooxygenase
hetero molecules

A: Putative antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,14714
Polymers24,6152
Non-polymers1,53212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area5270 Å2
ΔGint-67 kcal/mol
Surface area10160 Å2
MethodPISA
2
A: Putative antibiotic biosynthesis monooxygenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)78,44142
Polymers73,8456
Non-polymers4,59636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area19650 Å2
ΔGint-234 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.740, 70.740, 96.021
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-205-

P6G

21A-220-

HOH

31A-227-

HOH

41A-352-

HOH

51A-353-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative antibiotic biosynthesis monooxygenase / Putative flavoredoxin


Mass: 12307.491 Da / Num. of mol.: 1 / Fragment: sequence database residues 28-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_1394 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A7Y0

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Non-polymers , 5 types, 145 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (28-131) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (28-131) WAS EXPRESSED WITH THE 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: 1.88 Å3/Da / Density % sol: 34.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2000M Ca(OAc)2, 40.0000% PEG-400, 0.1M HEPES pH 7.5, 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: 0.97919
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.3→29.185 Å / Num. obs: 22848 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.0562 % / Biso Wilson estimate: 13.027 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.03
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.3-1.350.569213986449594.7
1.35-1.40.4412.914811404999.9
1.4-1.460.333.915388417999.9
1.46-1.540.2285.716991458099.9
1.54-1.640.1558.117005455799.9
1.64-1.760.10611.5157324187100
1.76-1.940.06418.216986450399.8
1.94-2.220.0426.916716441499.8
2.22-2.80.02935.6169154439100
2.8-29.1850.02344.516691439699.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→29.185 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.08 / SU B: 1.479 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.051
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 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. CALCIUM IONS (CA) FROM THE CRYSTALLIZATION SOLUTIONS HAVE BEEN MODELED INTO THE STRUCTURE BASED ON METAL EXCITATION SCAN AND COORDINATION GEOMETRY. 4. ETHYLENE GLYCOL (EDO) AND POLYETHYLENE GLYCOL (PEG AND P6G) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1174 5.1 %RANDOM
Rwork0.135 ---
obs0.136 22844 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.74 Å2 / Biso mean: 15.901 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.41 Å20 Å2
2---0.82 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 54 147 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221042
X-RAY DIFFRACTIONr_bond_other_d0.0050.02777
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.0481414
X-RAY DIFFRACTIONr_angle_other_deg0.89831939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2685140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43225.21746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.80215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.141156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02178
X-RAY DIFFRACTIONr_mcbond_it1.1041.5593
X-RAY DIFFRACTIONr_mcbond_other0.4581.5228
X-RAY DIFFRACTIONr_mcangle_it1.7442984
X-RAY DIFFRACTIONr_scbond_it2.5123449
X-RAY DIFFRACTIONr_scangle_it3.8014.5409
X-RAY DIFFRACTIONr_rigid_bond_restr0.51411819
X-RAY DIFFRACTIONr_sphericity_free9.5235149
X-RAY DIFFRACTIONr_sphericity_bonded4.14351788
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 80 -
Rwork0.217 1509 -
all-1589 -
obs--94.47 %

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