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- PDB-5jjp: Crystal structure of CmiS6 -

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Basic information

Entry
Database: PDB / ID: 5jjp
TitleCrystal structure of CmiS6
ComponentsNonribosomal peptide synthase
KeywordsLIGASE / Five-layered alpha-beta-alpha-beta-alpha sandwich fold / ATP-binding
Function / homologyD-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 / Nonribosomal peptide synthase
Function and homology information
Biological speciesStreptomyces sp. MJ635-86F5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Nonribosomal peptide synthase
B: Nonribosomal peptide synthase
C: Nonribosomal peptide synthase
D: Nonribosomal peptide synthase


Theoretical massNumber of molelcules
Total (without water)234,5274
Polymers234,5274
Non-polymers00
Water9,170509
1
A: Nonribosomal peptide synthase


Theoretical massNumber of molelcules
Total (without water)58,6321
Polymers58,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nonribosomal peptide synthase


Theoretical massNumber of molelcules
Total (without water)58,6321
Polymers58,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nonribosomal peptide synthase


Theoretical massNumber of molelcules
Total (without water)58,6321
Polymers58,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nonribosomal peptide synthase


Theoretical massNumber of molelcules
Total (without water)58,6321
Polymers58,6321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Nonribosomal peptide synthase
D: Nonribosomal peptide synthase


Theoretical massNumber of molelcules
Total (without water)117,2642
Polymers117,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-16 kcal/mol
Surface area32560 Å2
MethodPISA
6
B: Nonribosomal peptide synthase
C: Nonribosomal peptide synthase


Theoretical massNumber of molelcules
Total (without water)117,2642
Polymers117,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-16 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.290, 109.210, 198.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA3 - 42319 - 439
21PROPROBB3 - 42319 - 439
12SERSERAA2 - 42318 - 439
22SERSERCC2 - 42318 - 439
13SERSERAA2 - 42318 - 439
23SERSERDD2 - 42318 - 439
14PROPROBB3 - 42319 - 439
24PROPROCC3 - 42319 - 439
15PROPROBB3 - 42319 - 439
25PROPRODD3 - 42319 - 439
16SERSERCC2 - 42318 - 439
26SERSERDD2 - 42318 - 439

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Nonribosomal peptide synthase


Mass: 58631.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. MJ635-86F5 (bacteria) / Gene: cmiS6 / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X5IJ97
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 1.95 Å3/Da / Density % sol: 36.84 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG20000, MES, magnesium chloride

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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: Dec 21, 2014
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: 2.3→56.45 Å / Num. obs: 81297 / % possible obs: 99.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 3 / % possible all: 98.9

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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: 3WV4

3wv4


Resolution: 2.3→55.43 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.86 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.234 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24368 4062 5 %RANDOM
Rwork0.20647 ---
obs0.20828 77160 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---1.92 Å2-0 Å2
3---2.65 Å2
Refinement stepCycle: 1 / Resolution: 2.3→55.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12438 0 0 509 12947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912752
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212216
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.98517388
X-RAY DIFFRACTIONr_angle_other_deg1.227328023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18651626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22821.881553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.661151854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.01215140
X-RAY DIFFRACTIONr_chiral_restr0.0950.21932
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114521
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022905
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)
11A243910.08
12B243910.08
21A231340.06
22C231340.06
31A244640.08
32D244640.08
41B231090.07
42C231090.07
51B245650.07
52D245650.07
61C234480.05
62D234480.05
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 292 -
Rwork0.259 5623 -
obs--98.71 %

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