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- PDB-2ril: Crystal structure of a putative monooxygenase (YP_001095275.1) fr... -

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Basic information

Entry
Database: PDB / ID: 2ril
TitleCrystal structure of a putative monooxygenase (YP_001095275.1) from Shewanella loihica PV-4 at 1.26 A resolution
ComponentsAntibiotic biosynthesis monooxygenase
KeywordsOXIDOREDUCTASE / YP_001095275.1 / Putative monooxygenase / Antibiotic biosynthesis monooxygenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


monooxygenase activity
Similarity search - Function
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 / S-1,2-PROPANEDIOL / Antibiotic biosynthesis monooxygenase
Similarity search - Component
Biological speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.26 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of A Putative Monooxygenase (YP_001095275.1) from Shewanella loihica PV-4 at 1.26 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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 1.4Jan 25, 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4614
Polymers11,2901
Non-polymers1713
Water1,982110
1
A: Antibiotic biosynthesis monooxygenase
hetero molecules

A: Antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9228
Polymers22,5802
Non-polymers3416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.931, 63.155, 27.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit of this protein has not been experimentally determined at the time of deposition.

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Components

#1: Protein Antibiotic biosynthesis monooxygenase


Mass: 11290.241 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: PV-4 / Gene: YP_001095275.1, Shew_3150 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QHR8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9797, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97971
30.97951
ReflectionResolution: 1.26→26.528 Å / Num. obs: 14880 / % possible obs: 63.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.26-1.2911.3140.753521.3143.1
1.29-1.331.20.1953.72131760.19510.7
1.33-1.371.30.1724.14653560.17222.3
1.37-1.411.50.1963.78925800.19637.8
1.41-1.451.80.193.713687500.1950.3
1.45-1.512.60.1654.624029110.16561.8
1.51-1.562.80.1364.7290810320.13673.2
1.56-1.633.10.1226.1324210550.12277.6
1.63-1.73.30.0977.4366711280.09784.4
1.7-1.783.40.0858392511540.08592.5
1.78-1.883.60.0847.8409411380.08493.6
1.88-1.993.70.0758.5389010620.07593
1.99-2.133.70.0667.436439890.06691.9
2.13-2.33.60.0636.434199380.06391.9
2.3-2.523.70.0619.531168440.06190.3
2.52-2.823.60.069.828097710.0689.9
2.82-3.253.60.05510.223826640.05587.4
3.25-3.983.30.04811.118965660.04885.8
3.98-5.633.80.04612.317644610.04687.5
5.63-26.5283.50.0539.38982530.05382.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.26→26.528 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.555 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.063
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. ACETATE, CHLORIDE, AND PGO WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 4. CSD WAS MODELED BASED ON DENSITY. 5. THE NOMINAL RESOLUTION IS 1.50 A WITH 2718 OBSERVED REFLECTIONS BETWEEN 1.50-1.26 (28.8% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.162 742 5 %RANDOM
Rwork0.14 ---
obs0.141 14848 63.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.65 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.26→26.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 10 110 868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022849
X-RAY DIFFRACTIONr_bond_other_d0.0020.02559
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9541162
X-RAY DIFFRACTIONr_angle_other_deg0.96231368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92624.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40415137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.783155
X-RAY DIFFRACTIONr_chiral_restr0.1060.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02990
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02173
X-RAY DIFFRACTIONr_nbd_refined0.2160.2166
X-RAY DIFFRACTIONr_nbd_other0.1980.2566
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2412
X-RAY DIFFRACTIONr_nbtor_other0.0880.2467
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.215
X-RAY DIFFRACTIONr_mcbond_it1.7751.5578
X-RAY DIFFRACTIONr_mcbond_other0.6631.5206
X-RAY DIFFRACTIONr_mcangle_it2.182846
X-RAY DIFFRACTIONr_scbond_it3.3863361
X-RAY DIFFRACTIONr_scangle_it4.384.5316
X-RAY DIFFRACTIONr_rigid_bond_restr2.18631629
X-RAY DIFFRACTIONr_sphericity_free8.4183111
X-RAY DIFFRACTIONr_sphericity_bonded3.3631385
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.625 1 -
Rwork0.24 51 -
all-52 -
obs--3.03 %

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