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- PDB-6ijb: Structure of 3-methylmercaptopropionate CoA ligase mutant K523A i... -

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Basic information

Entry
Database: PDB / ID: 6ijb
TitleStructure of 3-methylmercaptopropionate CoA ligase mutant K523A in complex with AMP and MMPA
ComponentsAMP-binding domain protein
KeywordsLIGASE / CoA ligase / ATP dependent / comformational change
Function / homology
Function and homology information


ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme ...ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(methylsulfanyl)propanoic acid / ADENOSINE MONOPHOSPHATE / AMP-binding domain protein
Similarity search - Component
Biological speciesRuegeria lacuscaerulensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.111 Å
AuthorsShao, X. / Cao, H.Y. / Wang, P. / Li, C.Y. / Zhao, F. / Peng, M. / Chen, X.L. / Zhang, Y.Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)31630012 China
National Science Foundation (China)41706152 China
National Science Foundation (China)31728001 China
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Mechanistic insight into 3-methylmercaptopropionate metabolism and kinetical regulation of demethylation pathway in marine dimethylsulfoniopropionate-catabolizing bacteria.
Authors: Shao, X. / Cao, H.Y. / Zhao, F. / Peng, M. / Wang, P. / Li, C.Y. / Shi, W.L. / Wei, T.D. / Yuan, Z. / Zhang, X.H. / Chen, X.L. / Todd, J.D. / Zhang, Y.Z.
History
DepositionOct 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMP-binding domain protein
B: AMP-binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5645
Polymers118,8152
Non-polymers7503
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-34 kcal/mol
Surface area41150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.467, 122.572, 74.260
Angle α, β, γ (deg.)90.00, 93.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AMP-binding domain protein / 3-methylmercaptopropionate CoA ligase / MMPA CoA ligase


Mass: 59407.371 Da / Num. of mol.: 2 / Mutation: K523A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria lacuscaerulensis (strain DSM 11314 / KCTC 2953 / ITI-1157) (bacteria)
Strain: DSM 11314 / KCTC 2953 / ITI-1157 / Gene: SL1157_2728 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0CPY8
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-A8C / 3-(methylsulfanyl)propanoic acid


Mass: 120.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris propane, PEG 3350, Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.11→26.18 Å / Num. obs: 65209 / % possible obs: 98.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 33.14
Reflection shellResolution: 2.11→2.19 Å / Rmerge(I) obs: 0.373 / Num. unique obs: 5614

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BSR

5bsr


Resolution: 2.111→26.18 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.2243 3151 4.84 %
Rwork0.1856 --
obs0.1875 65111 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.111→26.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8320 0 49 595 8964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088564
X-RAY DIFFRACTIONf_angle_d0.9611657
X-RAY DIFFRACTIONf_dihedral_angle_d16.0485110
X-RAY DIFFRACTIONf_chiral_restr0.0541298
X-RAY DIFFRACTIONf_plane_restr0.0071509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1111-2.14260.2986840.24411733X-RAY DIFFRACTION63
2.1426-2.17610.32991390.21982784X-RAY DIFFRACTION100
2.1761-2.21180.28821520.22832732X-RAY DIFFRACTION100
2.2118-2.24990.27671440.26432729X-RAY DIFFRACTION99
2.2499-2.29080.46911230.34712638X-RAY DIFFRACTION95
2.2908-2.33490.25851570.22482769X-RAY DIFFRACTION100
2.3349-2.38250.25631450.21252720X-RAY DIFFRACTION100
2.3825-2.43430.28091210.19682796X-RAY DIFFRACTION100
2.4343-2.49090.241380.20172780X-RAY DIFFRACTION100
2.4909-2.55320.26371430.20122754X-RAY DIFFRACTION100
2.5532-2.62220.25011440.20432761X-RAY DIFFRACTION100
2.6222-2.69930.26571390.21342724X-RAY DIFFRACTION99
2.6993-2.78630.27691440.20762777X-RAY DIFFRACTION100
2.7863-2.88590.25011630.20462724X-RAY DIFFRACTION99
2.8859-3.00130.22291510.19892770X-RAY DIFFRACTION100
3.0013-3.13780.23441310.20712760X-RAY DIFFRACTION100
3.1378-3.30310.24611350.2052769X-RAY DIFFRACTION100
3.3031-3.50980.21471480.1942720X-RAY DIFFRACTION98
3.5098-3.78030.24391300.18652692X-RAY DIFFRACTION97
3.7803-4.160.17661460.16122642X-RAY DIFFRACTION95
4.16-4.76020.18561130.13952691X-RAY DIFFRACTION96
4.7602-5.99060.18641390.15152722X-RAY DIFFRACTION97
5.9906-31.52750.1461220.14822773X-RAY DIFFRACTION97

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