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- PDB-4xrr: Crystal structure of cals8 from micromonospora echinospora (P294S... -

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Basic information

Entry
Database: PDB / ID: 4xrr
TitleCrystal structure of cals8 from micromonospora echinospora (P294S mutant)
ComponentsCalS8
KeywordsOXIDOREDUCTASE / calicheamicin / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / polysaccharide biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
UDP-N-acetyl-D-mannosamine/glucosamine dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-N-acetyl-D-mannosamine/glucosamine dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMichalska, K. / Bigelow, L. / Endres, M. / Babnigg, G. / Bingman, C.A. / Yennamalli, R.M. / Singh, S. / Kharel, M.K. / Thorson, J.S. / Phillips Jr., G.N. ...Michalska, K. / Bigelow, L. / Endres, M. / Babnigg, G. / Bingman, C.A. / Yennamalli, R.M. / Singh, S. / Kharel, M.K. / Thorson, J.S. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: J. Biol. Chem. / Year: 2015
Title: Structural Characterization of CalS8, a TDP-alpha-D-Glucose Dehydrogenase Involved in Calicheamicin Aminodideoxypentose Biosynthesis.
Authors: Singh, S. / Michalska, K. / Bigelow, L. / Endres, M. / Kharel, M.K. / Babnigg, G. / Yennamalli, R.M. / Bingman, C.A. / Joachimiak, A. / Thorson, J.S. / Phillips, G.N.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 11, 2015ID: 4WB1
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 2.0Nov 8, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_poly / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalS8
B: CalS8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1763
Polymers96,0842
Non-polymers921
Water1,53185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-45 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.392, 88.200, 70.936
Angle α, β, γ (deg.)90.00, 103.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CalS8


Mass: 48041.793 Da / Num. of mol.: 2 / Mutation: P294S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calS8 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: Q8KNF6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M magnesium formate, 15% PEG 3350, pH 8.0, Temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 13, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 27596 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 53.08 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.6
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.74 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
MR-Rosettaphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gg2

3gg2


Resolution: 2.55→37.16 Å / Cor.coef. Fo:Fc: 0.9339 / Cor.coef. Fo:Fc free: 0.9012 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1128 4.09 %RANDOM
Rwork0.1835 ---
obs0.1853 27580 99.8 %-
Displacement parametersBiso mean: 49.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.6104 Å20 Å2-4.1491 Å2
2---4.5702 Å20 Å2
3---3.9598 Å2
Refine analyzeLuzzati coordinate error obs: 0.339 Å
Refinement stepCycle: 1 / Resolution: 2.55→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 6 85 6731
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016766HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.819224HARMONIC3
X-RAY DIFFRACTIONt_dihedral_angle_d3074SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1036HARMONIC5
X-RAY DIFFRACTIONt_it6766HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion2.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion889SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7900SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.65 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.262 112 3.91 %
Rwork0.2145 2751 -
all0.2163 2863 -
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)
11.8547-1.0881-0.83662.26640.88291.3882-0.1679-0.11960.30450.05140.1964-0.2781-0.0374-0.0401-0.0284-0.0292-0.0023-0.055-0.0108-0.0584-0.066719.089529.784395.539
21.9625-0.82730.86092.54820.04961.2786-0.14-0.2913-0.00240.25010.1842-0.19190.07330.0271-0.0442-0.00120.00860.008-0.01230.0158-0.13911.212523.558393.4479
3-0.05532.01431.28760-2.42590.61710.0030.09660.1855-0.08570.0459-0.0027-0.01710.0727-0.04890.10710.14730.17090.14240.0193-0.017417.626233.465978.4585
40.4723-0.21450.42121.1743-0.26251.61860.07070.02070.04040.04390.09640.0024-0.2886-0.0971-0.1671-0.0856-0.0427-0.002-0.07950.0007-0.0685.981432.266272.2995
50.9104-0.2494-0.19061.59910.17230.27930.0532-0.2192-0.18950.0423-0.05340.03280.16210.10260.0002-0.0035-0.0313-0.0532-0.01240.0175-0.05388.275318.229261.5821
63.86450.1720.1394.0729-0.76012.38140.0723-0.4629-0.29390.086-0.3039-0.28820.09350.44910.2316-0.19030.02860.010.03910.096-0.11628.094118.989256.906
74.1846-1.63072.14894.5640.74924.03530.0719-0.03660.09280.26590.01050.3472-0.4901-0.5682-0.0824-0.2250.0972-0.03130.02780.0834-0.1155-5.203254.135238.8487
81.6148-0.0860.9543.2615-1.19552.6790.12420.38480.2228-0.4265-0.03260.4578-0.0068-0.4678-0.0916-0.16540.0496-0.06580.01640.0204-0.1433-3.814143.037634.1214
90.6682-0.51980.11380.15081.48520.4023-0.015-0.04390.0235-0.01450.0557-0.010.0155-0.0789-0.04070.11470.02490.11170.1428-0.04260.0362-3.721150.18454.3916
100.6192-0.2137-0.0820.9538-1.08871.97770.04240.01770.05810.02550.08330.0418-0.1711-0.119-0.1258-0.0623-0.0346-0.0136-0.0373-0.0133-0.05222.207837.188957.2246
114.4413-0.956-1.20062.4278-0.32423.51620.02270.1291-0.2341-0.39230.36340.43710.0626-0.2129-0.3861-0.155-0.1373-0.117-0.06160.1091-0.01-12.333324.96359.3559
126.5551-1.1261.95153.6097-2.71366.5558-0.0759-0.1462-0.13680.27690.3060.3142-0.5462-0.5944-0.2301-0.33770.11260.05270.01510.1831-0.1525-24.312439.840467.81
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-2 - A|55}
2X-RAY DIFFRACTION2{A|56 - A|163}
3X-RAY DIFFRACTION3{A|164 - A|178}
4X-RAY DIFFRACTION4{A|179 - A|257}
5X-RAY DIFFRACTION5{A|258 - A|328}
6X-RAY DIFFRACTION6{A|329 - A|453}
7X-RAY DIFFRACTION7{B|-2 - B|65}
8X-RAY DIFFRACTION8{B|66 - B|166}
9X-RAY DIFFRACTION9{B|167 - B|178}
10X-RAY DIFFRACTION10{B|179 - B|271}
11X-RAY DIFFRACTION11{B|272 - B|327}
12X-RAY DIFFRACTION12{B|328 - B|453}

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