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- PDB-6omr: Crystal structure of PtmU3 complexed with PTN substrate -

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Basic information

Entry
Database: PDB / ID: 6omr
TitleCrystal structure of PtmU3 complexed with PTN substrate
ComponentsPtmU3
KeywordsOXIDOREDUCTASE / TIM-barrel
Function / homology
Function and homology information


organic substance metabolic process / carboxy-lyase activity / hydrolase activity
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
ACETATE ION / : / Chem-MYM / PtmU3
Similarity search - Component
Biological speciesStreptomyces platensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsLiu, Y.C. / Dong, L.B. / Shen, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114353 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Characterization and Crystal Structure of a Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis.
Authors: Dong, L.B. / Liu, Y.C. / Cepeda, A.J. / Kalkreuter, E. / Deng, M.R. / Rudolf, J.D. / Chang, C. / Joachimiak, A. / Phillips Jr., G.N. / Shen, B.
History
DepositionApr 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PtmU3
B: PtmU3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,99512
Polymers78,8252
Non-polymers1,17010
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimeric form
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-56 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.620, 122.420, 140.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-534-

HOH

21B-667-

HOH

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Components

#1: Protein PtmU3


Mass: 39412.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis (bacteria) / Plasmid: pRSF/TEV/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A0UVH9
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MYM / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (5beta,7alpha,8alpha,10alpha,12alpha)-7-hydroxyatis-16-ene-18-thioate


Mass: 658.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H51N2O9PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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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: 3.09 Å3/Da / Density % sol: 60.19 % / Mosaicity: 0.47 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris propane pH 7.0, 2.8 M Sodium acetate trihydrate, 4 mM Manganese

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 8, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 36210 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Χ2: 0.892 / Net I/σ(I): 14.3 / Num. measured all: 267001
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.497.30.8917910.7790.3520.9580.935100
2.49-2.547.30.84517910.8180.3340.9090.947100
2.54-2.597.30.65117970.8660.2580.70.954100
2.59-2.647.40.53617560.9120.2110.5760.934100
2.64-2.77.40.47318070.930.1860.5080.932100
2.7-2.767.40.41117670.9410.1620.4420.902100
2.76-2.837.40.33418050.9580.1320.360.952100
2.83-2.97.40.25418010.9750.10.2730.893100
2.9-2.997.40.19117970.9870.0750.2050.912100
2.99-3.097.40.16217810.9880.0640.1740.89100
3.09-3.27.40.12718160.9940.050.1360.919100
3.2-3.327.40.08718060.9970.0340.0930.927100
3.32-3.487.40.06718030.9980.0260.0720.911100
3.48-3.667.40.0518150.9980.020.0540.92100
3.66-3.897.50.03718150.9990.0150.040.899100
3.89-4.197.40.0318150.9990.0120.0330.887100
4.19-4.617.40.024180710.0090.0250.863100
4.61-5.277.40.02218440.9990.0090.0230.794100
5.27-6.637.30.02118570.9990.0080.0220.729100
6.63-3070.0219390.9980.0090.0220.75399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OMP

6omp


Resolution: 2.45→29.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.726 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.356 / ESU R Free: 0.265
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1679 4.8 %RANDOM
Rwork0.182 ---
obs0.1852 33563 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.11 Å2 / Biso mean: 38.853 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.55 Å2
Refinement stepCycle: final / Resolution: 2.45→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 65 321 5932
Biso mean--65.67 35.75 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135756
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175333
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6537873
X-RAY DIFFRACTIONr_angle_other_deg1.3231.58912275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77320.554325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67615870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0421558
X-RAY DIFFRACTIONr_chiral_restr0.0690.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026544
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021284
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 100 -
Rwork0.296 1950 -
all-2050 -
obs--77.71 %

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