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Basic information

Entry
Database: PDB / ID: 5uhj
TitleThe crystal structure of a natural product biosynthetic enzyme from Streptomyces sp. CB03234
ComponentsGlyoxalase/bleomycin resisance protein/dioxygenase
KeywordsOXIDOREDUCTASE / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


dioxygenase activity
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Glyoxalase/bleomycin resisance protein/dioxygenase
Similarity search - Component
Biological speciesStreptomyces sp. CB03234 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsTan, K. / Li, H. / Endres, M. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: The crystal structure of a natural product biosynthetic enzyme from Streptomyces sp. CB03234
Authors: Tan, K. / Li, H. / Endres, M. / Phillips Jr., G.N. / Joachimiak, A.
History
DepositionJan 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 23, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase/bleomycin resisance protein/dioxygenase
B: Glyoxalase/bleomycin resisance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3923
Polymers29,3462
Non-polymers461
Water2,522140
1
A: Glyoxalase/bleomycin resisance protein/dioxygenase
hetero molecules

A: Glyoxalase/bleomycin resisance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4384
Polymers29,3462
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3400 Å2
ΔGint-20 kcal/mol
Surface area11520 Å2
MethodPISA
2
B: Glyoxalase/bleomycin resisance protein/dioxygenase

B: Glyoxalase/bleomycin resisance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)29,3462
Polymers29,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3250 Å2
ΔGint-19 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.836, 33.346, 101.781
Angle α, β, γ (deg.)90.00, 98.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glyoxalase/bleomycin resisance protein/dioxygenase


Mass: 14672.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CB03234 (bacteria) / Gene: tnmS1 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0A125SA24
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 0.2 M Magnesium Formate, 20% (w/v) PEG3500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 5, 2016 / Details: mirror
RadiationMonochromator: Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.75→35 Å / Num. obs: 27985 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.031 / Net I/σ(I): 21
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) all: 1.6 / Num. unique all: 1375 / CC1/2: 0.608 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→30.886 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2432 1359 5.07 %
Rwork0.194 --
obs0.1964 26781 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→30.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 3 140 2050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141947
X-RAY DIFFRACTIONf_angle_d1.2692640
X-RAY DIFFRACTIONf_dihedral_angle_d16.3471159
X-RAY DIFFRACTIONf_chiral_restr0.088297
X-RAY DIFFRACTIONf_plane_restr0.008351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.81250.2767840.25121557X-RAY DIFFRACTION59
1.8125-1.88510.2521250.21582449X-RAY DIFFRACTION92
1.8851-1.97090.26561630.2062649X-RAY DIFFRACTION100
1.9709-2.07480.23151490.18952631X-RAY DIFFRACTION100
2.0748-2.20470.25731470.18352648X-RAY DIFFRACTION100
2.2047-2.37490.25851320.18962689X-RAY DIFFRACTION100
2.3749-2.61380.23511430.19272672X-RAY DIFFRACTION100
2.6138-2.99170.27271360.20862692X-RAY DIFFRACTION100
2.9917-3.76820.21991380.18292699X-RAY DIFFRACTION100
3.7682-30.89060.23541420.19142736X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.95070.48490.0081.85590.41752.3879-0.08420.5102-0.1345-0.0470.0950.10430.0527-0.6279-0.02310.0610.0214-0.00430.14260.01690.1557-9.1514-16.049-1.1619
26.9508-0.02730.04594.9608-3.23067.54990.1010.9625-0.156-0.6308-0.01250.45030.1723-0.6461-0.10840.10550.0926-0.02220.29660.00450.2707-15.5435-13.6854-3.669
34.19731.4961-0.5811.9793-0.88283.82890.16710.3445-0.1805-0.3322-0.1024-0.30760.1339-0.6241-0.07230.10340.00540.02520.16880.01440.2164-9.6918-16.0406-3.7575
42.95560.072-1.09724.16940.76765.1798-0.0147-0.306-0.19840.27980.1153-0.30180.12410.1291-0.0780.08380.0098-0.00630.13620.02280.1496-5.3698-18.100512.6127
56.1884-0.73012.31521.49531.17742.3691-0.0524-0.853-0.28740.30860.57670.07450.8051-0.2989-0.23610.48920.0015-0.08630.2190.02180.1939-4.8821-23.441760.6002
63.2102-0.23661.01682.87720.52925.2491-0.2356-0.29530.2944-0.06360.01330.4372-0.4144-1.81830.02140.26670.0614-0.01010.49880.01840.1698-20.8736-12.471144.5982
72.19310.4668-1.04063.8815-2.31591.67370.0173-0.82880.29630.44610.2860.52660.6707-1.87780.06940.3158-0.1444-0.02250.94270.00820.3048-23.4866-18.169849.1638
84.2781-2.16550.52195.1448-0.96054.07770.2288-0.2432-0.53950.0538-0.1040.06410.7572-0.7785-0.10430.393-0.1512-0.10160.27070.04570.171-16.3042-21.357349.697
95.4207-1.959-0.07948.0480.85185.24720.0226-0.21770.68220.6497-0.2153-0.0247-0.4892-1.05120.02840.35440.0789-0.03650.39340.01830.2341-19.55-9.803352.6939
100.5518-0.55120.6381.0229-1.62263.7387-0.1937-0.32150.20860.62940.31030.1811-1.3157-0.53060.01740.93610.1247-0.07180.26870.04090.3222-13.32-2.630549.2513
113.6182-0.9655-0.19556.02233.0751.62160.06180.26420.2379-0.0130.2994-0.48170.20950.4721-0.12740.3890.0488-0.07380.1969-0.02180.1451-6.2061-18.768839.935
122.642-0.447-0.08013.03610.26195.3579-0.0740.454-0.0702-0.53820.13720.27480.5805-0.4209-0.1620.3006-0.0257-0.00070.2678-0.00950.0887-11.7839-19.586527.6902
136.55511.2161-0.39326.5086-0.73198.62660.14780.16370.34620.17780.13870.0439-0.7029-0.3042-0.0910.26290.0430.00540.2875-0.00070.0583-11.8506-11.535831.2285
146.4674-7.3341-0.13449.29580.71660.32980.35140.51211.0006-0.3315-0.4556-1.5339-0.28572.1254-0.15440.24590.03070.03460.78420.09950.35290.4774-15.399830.5866
156.1313-2.7886-1.69126.77131.09538.21210.29190.14050.3714-0.17380.1063-0.5301-0.3790.3591-0.27560.248-0.001-0.04780.1631-0.0220.125-8.354-13.198337.4766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 125 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 6 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 40 )
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 61 )
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 80 )
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 97 )
14X-RAY DIFFRACTION14chain 'B' and (resid 98 through 107 )
15X-RAY DIFFRACTION15chain 'B' and (resid 108 through 125 )

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