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- PDB-3fgv: CRYSTAL STRUCTURE OF A PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGE... -

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Basic information

Entry
Database: PDB / ID: 3fgv
TitleCRYSTAL STRUCTURE OF A PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE (SPO2313) FROM SILICIBACTER POMEROYI DSS-3 AT 1.30 A RESOLUTION
Componentsuncharacterized protein with ferredoxin-like fold
KeywordsOXIDOREDUCTASE / PHOSPHOSERINE AMINOTRANSFERASE SERC / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyAntibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Unknown ligand / ABM domain-containing protein
Function and homology information
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function with ferredoxin-like fold (YP_167536.1) from SILICIBACTER POMEROYI DSS-3 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: 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 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: uncharacterized protein with ferredoxin-like fold
B: uncharacterized protein with ferredoxin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,12318
Polymers24,8132
Non-polymers31016
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint2 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.760, 78.760, 69.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein uncharacterized protein with ferredoxin-like fold


Mass: 12406.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Gene: SPO2313, YP_167536.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LR19
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 11 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2000M NH4I, 20.0000% PEG-3350, No Buffer pH 6.2, 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 11, 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: 1.3→26.118 Å / Num. obs: 60325 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.966 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.22
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.3-1.350.4352.6402361229996.6
1.35-1.40.3513.5405601080598.1
1.4-1.460.2854.4420861115598.3
1.46-1.540.2135.8461601221698.6
1.54-1.640.1458.4465211223898.8
1.64-1.760.10611.2428601124599.1
1.76-1.940.07315.6460451203699.1
1.94-2.220.05321.5454971186399.4
2.22-2.80.06128.3714211193599.7
2.8-26.1180.04539.7923231195499.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PHENIXrefinement
SOLVEphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.3→26.118 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.128 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.039
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE OF EACH MONOMER. IODIDE ION FROM NH4I USED IN CRYSTALLIZATION CONDITION MAY ACCOUNT FOR THE ANOMALOUS DIFFERENCE DENSITY SORROUNDING ONE OR MORE ATOMS OF UNL. 4. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.15 3041 5 %RANDOM
Rwork0.13 ---
obs0.131 60282 99.87 %-
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: 55.86 Å2 / Biso mean: 14.97 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 31 289 1856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221928
X-RAY DIFFRACTIONr_bond_other_d0.0050.021379
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.982670
X-RAY DIFFRACTIONr_angle_other_deg1.6933406
X-RAY DIFFRACTIONTORSION ANGLES, PERUNL 1 (DEGREES)5.2855273
X-RAY DIFFRACTIONTORSION ANGLES, PERUNL 2 (DEGREES)34.88624.643112
X-RAY DIFFRACTIONTORSION ANGLES, PERUNL 3 (DEGREES)13.46215379
X-RAY DIFFRACTIONTORSION ANGLES, PERUNL 4 (DEGREES)17.181517
X-RAY DIFFRACTIONr_chiral_restr0.1090.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022230
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02411
X-RAY DIFFRACTIONr_nbd_refined0.1950.2347
X-RAY DIFFRACTIONr_nbd_other0.1650.21391
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2888
X-RAY DIFFRACTIONr_nbtor_other0.0820.21078
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0890.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.232
X-RAY DIFFRACTIONr_mcbond_it1.61121105
X-RAY DIFFRACTIONr_mcbond_other0.7932427
X-RAY DIFFRACTIONr_mcangle_it2.37641819
X-RAY DIFFRACTIONr_scbond_it3.5516904
X-RAY DIFFRACTIONr_scangle_it4.7248802
X-RAY DIFFRACTIONr_rigid_bond_restr1.31633681
X-RAY DIFFRACTIONr_sphericity_free6.1983313
X-RAY DIFFRACTIONr_sphericity_bonded3.08733226
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 215 -
Rwork0.172 4202 -
all-4417 -
obs--99.24 %

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