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- PDB-3e8o: CRYSTAL STRUCTURE OF A PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGE... -

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Basic information

Entry
Database: PDB / ID: 3e8o
TitleCRYSTAL STRUCTURE OF A PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE (DR_2100) FROM DEINOCOCCUS RADIODURANS AT 1.40 A RESOLUTION
Componentsuncharacterized protein with ferredoxin-like fold
KeywordsOXIDOREDUCTASE / PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE / 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
Unknown ligand / ABM domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function with ferredoxin-like fold (NP_295823.1) from DEINOCOCCUS RADIODURANS at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)26,4655
Polymers26,4022
Non-polymers623
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-30 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.715, 59.639, 47.511
Angle α, β, γ (deg.)90.000, 97.180, 90.000
Int Tables number4
Space group name H-MP1211
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: 13201.220 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: NP_295823.1, DR_2100 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9RSM4
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#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.: 271 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 1.79 Å3/Da / Density % sol: 31.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2000M NaOAc, 30.0000% PEG-8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97916,0.97849
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 1, 2008 / 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
20.979161
30.978491
ReflectionResolution: 1.4→29.814 Å / Num. obs: 35346 / % possible obs: 96.3 % / Redundancy: 2.1 % / Biso Wilson estimate: 13.442 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→29.814 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 1.877 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.056
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. EDO MOLECULE FROM THE CRYO SOLUTION IS MODELED. 4. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE
RfactorNum. reflection% reflectionSelection details
Rfree0.163 1784 5.1 %RANDOM
Rwork0.128 ---
obs0.13 35326 96.02 %-
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: 59.85 Å2 / Biso mean: 17.787 Å2 / Biso min: 7.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.3 Å2
2---0.34 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 16 271 1823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211621
X-RAY DIFFRACTIONr_bond_other_d0.0030.02996
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9442218
X-RAY DIFFRACTIONr_angle_other_deg1.74732476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9315217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17324.85368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55415269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.585154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02295
X-RAY DIFFRACTIONr_mcbond_it2.2821029
X-RAY DIFFRACTIONr_mcbond_other1.1772422
X-RAY DIFFRACTIONr_mcangle_it3.42141651
X-RAY DIFFRACTIONr_scbond_it4.6746592
X-RAY DIFFRACTIONr_scangle_it6.658559
X-RAY DIFFRACTIONr_rigid_bond_restr1.97432617
X-RAY DIFFRACTIONr_sphericity_free8.3423289
X-RAY DIFFRACTIONr_sphericity_bonded4.56832579
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 126 -
Rwork0.179 2425 -
all-2551 -
obs--94.94 %

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