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- PDB-6ihk: Structure of MMPA CoA ligase in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 6ihk
TitleStructure of MMPA CoA ligase in complex with ADP
ComponentsAMP-binding domain protein
KeywordsLIGASE / CoA ligase / ATP dependent / dimer
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, C-terminal domain superfamily ...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, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / AMP-binding domain protein
Similarity search - Component
Biological speciesRuegeria lacuscaerulensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.23 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
DepositionSep 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)119,3583
Polymers118,9312
Non-polymers4271
Water8,395466
1
B: AMP-binding domain protein
hetero molecules

A: AMP-binding domain protein


Theoretical massNumber of molelcules
Total (without water)119,3583
Polymers118,9312
Non-polymers4271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area7260 Å2
ΔGint-38 kcal/mol
Surface area40180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.424, 121.193, 73.559
Angle α, β, γ (deg.)90.00, 93.68, 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: 59465.473 Da / Num. of mol.: 2
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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
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
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.23→46.48 Å / Num. obs: 53256 / % possible obs: 99.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.41
Reflection shellResolution: 2.23→2.31 Å / Rmerge(I) obs: 0.337 / Num. unique obs: 4732

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.23→46.48 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.12
RfactorNum. reflection% reflection
Rfree0.2229 2657 4.99 %
Rwork0.1731 --
obs0.1755 53233 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.23→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8226 0 27 466 8719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088495
X-RAY DIFFRACTIONf_angle_d1.04311570
X-RAY DIFFRACTIONf_dihedral_angle_d16.415052
X-RAY DIFFRACTIONf_chiral_restr0.0571288
X-RAY DIFFRACTIONf_plane_restr0.0071501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2283-2.26880.28311130.22892066X-RAY DIFFRACTION77
2.2688-2.31240.26971450.20862671X-RAY DIFFRACTION100
2.3124-2.35960.26081400.19122736X-RAY DIFFRACTION100
2.3596-2.41090.25611510.18732647X-RAY DIFFRACTION100
2.4109-2.4670.23971420.19852673X-RAY DIFFRACTION100
2.467-2.52870.24311490.19322712X-RAY DIFFRACTION100
2.5287-2.59710.26161500.19152654X-RAY DIFFRACTION100
2.5971-2.67350.24521340.20092702X-RAY DIFFRACTION100
2.6735-2.75980.30881440.20132711X-RAY DIFFRACTION100
2.7598-2.85840.25451210.19772699X-RAY DIFFRACTION99
2.8584-2.97280.25791180.19252712X-RAY DIFFRACTION100
2.9728-3.10810.25031420.19172668X-RAY DIFFRACTION100
3.1081-3.27190.23141490.18762706X-RAY DIFFRACTION99
3.2719-3.47690.23021500.17732695X-RAY DIFFRACTION100
3.4769-3.74520.21771330.16522707X-RAY DIFFRACTION99
3.7452-4.12190.19981400.14512673X-RAY DIFFRACTION99
4.1219-4.71790.17911290.13082713X-RAY DIFFRACTION99
4.7179-5.94210.19511460.15742712X-RAY DIFFRACTION100
5.9421-46.74170.18391610.1712719X-RAY DIFFRACTION99

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