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- PDB-4xr9: Crystal structure of CalS8 from Micromonospora echinospora cocrys... -

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Basic information

Entry
Database: PDB / ID: 4xr9
TitleCrystal structure of CalS8 from Micromonospora echinospora cocrystallized with NAD and TDP-glucose
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / THYMIDINE-5'-PHOSPHATE / CalS8
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098248 United States
CitationJournal: To Be Published
Title: Crystal structure of CalS8 from Micromonospora echinospora
Authors: 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.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Other
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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: CalS8
B: CalS8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6226
Polymers95,5212
Non-polymers1,1014
Water5,242291
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-54 kcal/mol
Surface area33510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.682, 87.040, 70.660
Angle α, β, γ (deg.)90.00, 103.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CalS8


Mass: 47760.426 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

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Non-polymers , 5 types, 295 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 4.51 mM TDP-glucose, 4.51 mM NAD, 16% PEG 4000, 0.1 M TRIS pH 8.5, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979152 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2013 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979152 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 60172 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 31.82 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 22.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.22 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GG2

3gg2


Resolution: 1.95→28.19 Å / Cor.coef. Fo:Fc: 0.9529 / Cor.coef. Fo:Fc free: 0.9411 / SU R Cruickshank DPI: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 3044 5.06 %RANDOM
Rwork0.1711 ---
obs0.1728 60152 99.13 %-
Displacement parametersBiso mean: 40.83 Å2
Baniso -1Baniso -2Baniso -3
1-7.4749 Å20 Å21.9143 Å2
2---5.3826 Å20 Å2
3----2.0923 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.95→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6726 0 72 291 7089
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096928HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.749461HARMONIC3
X-RAY DIFFRACTIONt_dihedral_angle_d3153SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes136HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1080HARMONIC5
X-RAY DIFFRACTIONt_it6928HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion2.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion910SEMIHARMONIC5
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_contact8275SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2517 200 4.98 %
Rwork0.1989 3820 -
all0.2015 4020 -
obs--99.13 %
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)
11.1990.3756-1.25091.8144-1.40082.0652-0.02450.0002-0.052-0.36320.08810.20290.2727-0.0567-0.0636-0.0937-0.0656-0.0573-0.04160.0436-0.0487-19.18569.6444-38.3863
21.2936-1.46030.15390.9748-0.65092.6344-0.0826-0.01890.1125-0.2024-0.0185-0.04360.17340.13350.10110.0389-0.04160.0697-0.03970.0572-0.0285-7.928117.7991-49.7701
30.74690.08910.32181.3978-0.90261.5811-0.068-0.00220.14560.00240.30350.3113-0.1057-0.3961-0.2356-0.16740.0120.0198-0.0120.06710.0334-20.093820.3686-30.3271
4-0.20360.13881.8260.6213-1.27261.236-0.05380.12440.0636-0.1508-0.0110.13750.11340.10240.0648-0.1057-0.02360.0269-0.01940.01-0.0247-7.072510.1081-30.4738
51.41950.34130.41910.7995-0.24510.8025-0.0274-0.0732-0.040.01130.02680.02520.0217-0.04490.0007-0.0385-0.00010.0084-0.0653-0.0079-0.05754.448211.1365-22.5527
64.4446-0.0782-2.75271.0538-0.22.6339-0.0145-0.04790.1490.06620.02220.0654-0.1555-0.0182-0.00760.00290.0089-0.0331-0.0907-0.021-0.01479.664427.2837-20.674
71.1473-1.5944-0.62333.7691-0.02881.7638-0.0077-0.01820.09590.07360.0129-0.0306-0.2273-0.0577-0.0052-0.03330.0319-0.0028-0.06540.0334-0.074519.538827.6261-38.5745
81.4740.22460.01053.7706-1.63660.32120.01720.15710.16620.06170.06280.0301-0.2783-0.22-0.080.00560.0155-0.0125-0.10260.0408-0.044918.320431.5728-39.5327
91.3211-0.1867-0.3522.1079-0.07862.1623-0.00980.30180.1448-0.2411-0.01290.193-0.1405-0.08940.0227-0.04410.0112-0.0318-0.06060.0466-0.071618.337824.778-44.945
102.1472-0.2867-0.01441.272-0.26322.0250.0848-0.00860.0152-0.0255-0.0002-0.05520.0320.1932-0.0846-0.07410.01850.0074-0.02650.0342-0.037929.898417.738-38.7902
112.2786-0.92720.72142.3521-0.77791.9019-0.2232-0.3307-0.09560.50170.1674-0.0148-0.06060.03450.0559-0.09970.06750.0006-0.06750.0375-0.181932.5811-4.4311-6.0589
122.1755-0.7995-0.58240.7317-0.1020.86270.0156-0.2083-0.07190.0989-0.00810.0482-0.0955-0.0252-0.0076-0.02470.00040.0049-0.06730.0012-0.06077.762511.1834-12.6933
130.46050.13-0.88631.985-1.04842.3989-0.1181-0.08140.24350.34410.1803-0.1849-0.14990.1669-0.0622-0.0350.0154-0.0408-0.0948-0.0473-0.157111.673219.8131-3.7614
143.23430.06742.3062.7383-0.97964.58340.01290.0124-0.25060.15410.19520.1833-0.266-0.2795-0.2081-0.12160.04990.0556-0.14170.029-0.1675-1.27094.07438.2645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-2 - A|44}
2X-RAY DIFFRACTION2{A|45 - A|72}
3X-RAY DIFFRACTION3{A|73 - A|157}
4X-RAY DIFFRACTION4{A|158 - A|186}
5X-RAY DIFFRACTION5{A|187 - A|274}
6X-RAY DIFFRACTION6{A|275 - A|322}
7X-RAY DIFFRACTION7{A|323 - A|349}
8X-RAY DIFFRACTION8{A|350 - A|373}
9X-RAY DIFFRACTION9{A|374 - A|412}
10X-RAY DIFFRACTION10{A|413 - A|453}
11X-RAY DIFFRACTION11{B|-1 - B|210}
12X-RAY DIFFRACTION12{B|211 - B|279}
13X-RAY DIFFRACTION13{B|280 - B|322}
14X-RAY DIFFRACTION14{B|323 - B|453}

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