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- PDB-5jjq: Crystal structure of IdnL1 -

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Basic information

Entry
Database: PDB / ID: 5jjq
TitleCrystal structure of IdnL1
ComponentsAMP-dependent synthetase and ligase
KeywordsLIGASE / Five layered alpha-beta-alpha-beta-alpha sandwich fold / ATP-binding
Function / homology
Function and homology information


D-alanine:D-alanyl carrier protein ligase-like / 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. / AMP-dependent synthetase/ligase / AMP-binding enzyme
Similarity search - Domain/homology
Chem-6L1 / AMP-dependent synthetase and ligase
Similarity search - Component
Biological speciesStreptomyces sp. ML694-90F3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCieslak, J. / Miyanaga, A. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25850050 Japan
CitationJournal: Proteins / Year: 2017
Title: Biochemical characterization and structural insight into aliphatic beta-amino acid adenylation enzymes IdnL1 and CmiS6
Authors: Cieslak, J. / Miyanaga, A. / Takaku, R. / Takaishi, M. / Amagai, K. / Kudo, F. / Eguchi, T.
History
DepositionApr 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMP-dependent synthetase and ligase
B: AMP-dependent synthetase and ligase
C: AMP-dependent synthetase and ligase
D: AMP-dependent synthetase and ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,29112
Polymers236,4204
Non-polymers1,8718
Water4,450247
1
A: AMP-dependent synthetase and ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5733
Polymers59,1051
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-10 kcal/mol
Surface area21990 Å2
MethodPISA
2
B: AMP-dependent synthetase and ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5733
Polymers59,1051
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-10 kcal/mol
Surface area21630 Å2
MethodPISA
3
C: AMP-dependent synthetase and ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5733
Polymers59,1051
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-10 kcal/mol
Surface area22170 Å2
MethodPISA
4
D: AMP-dependent synthetase and ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5733
Polymers59,1051
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.750, 104.450, 120.000
Angle α, β, γ (deg.)81.78, 83.01, 81.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA9 - 50829 - 528
21ALAALABB9 - 50829 - 528
12ALAALAAA9 - 50829 - 528
22ALAALACC9 - 50829 - 528
13ALAALAAA9 - 50829 - 528
23ALAALADD9 - 50829 - 528
14ALAALABB9 - 50829 - 528
24ALAALACC9 - 50829 - 528
15VALVALBB5 - 50825 - 528
25VALVALDD5 - 50825 - 528
16ALAALACC9 - 50829 - 528
26ALAALADD9 - 50829 - 528

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
AMP-dependent synthetase and ligase


Mass: 59104.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. ML694-90F3 (bacteria) / Gene: idnL1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A077KT11
#2: Chemical
ChemComp-6L1 / 5'-O-[(R)-{[(3S)-3-aminobutanoyl]oxy}(hydroxy)phosphoryl]adenosine


Mass: 432.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H21N6O8P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG3350, sodium citrate, potassium chloride, ATP, magnesium chloride, (S)-3-aminobutyrate, Tris, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→59.51 Å / Num. obs: 90052 / % possible obs: 94.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLM1.0.7data reduction
SCALA3.3.20data scaling
MOLREP11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JJP

5jjp


Resolution: 2.6→59.51 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.499 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.301 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26517 4516 5 %RANDOM
Rwork0.23376 ---
obs0.23532 85526 94.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.721 Å2
Baniso -1Baniso -2Baniso -3
1--6.02 Å2-1.7 Å2-1.44 Å2
2--4.08 Å22.73 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.6→59.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14718 0 120 247 15085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01915224
X-RAY DIFFRACTIONr_bond_other_d0.0060.0214597
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.99320751
X-RAY DIFFRACTIONr_angle_other_deg1.1513.00333512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81551944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29222.168641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37152281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.98315162
X-RAY DIFFRACTIONr_chiral_restr0.090.22345
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02117271
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023419
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A288910.06
12B288910.06
21A291820.06
22C291820.06
31A284830.07
32D284830.07
41B288660.06
42C288660.06
51B289980.06
52D289980.06
61C284250.07
62D284250.07
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 373 -
Rwork0.345 6318 -
obs--94.68 %

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