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- PDB-5ocd: structure of a CDPS from Fluoribacter dumoffii -

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Basic information

Entry
Database: PDB / ID: 5ocd
Titlestructure of a CDPS from Fluoribacter dumoffii
ComponentsCyclodipeptide synthase
KeywordsRNA BINDING PROTEIN / Non ribosomal peptide synthesis / tRNA / CDPS
Function / homology:
Function and homology information
Biological speciesFluoribacter dumoffii NY 23 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsSchmitt, E. / Mechulam, Y. / Bourgeois, G.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural basis for partition of the cyclodipeptide synthases into two subfamilies.
Authors: Bourgeois, G. / Seguin, J. / Babin, M. / Belin, P. / Moutiez, M. / Mechulam, Y. / Gondry, M. / Schmitt, E.
History
DepositionJun 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Cyclodipeptide synthase
B: Cyclodipeptide synthase
C: Cyclodipeptide synthase
D: Cyclodipeptide synthase
E: Cyclodipeptide synthase
F: Cyclodipeptide synthase
G: Cyclodipeptide synthase
H: Cyclodipeptide synthase
I: Cyclodipeptide synthase
J: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)313,52610
Polymers313,52610
Non-polymers00
Water1,00956
1
A: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)31,3531
Polymers31,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)185.031, 97.800, 211.282
Angle α, β, γ (deg.)90.00, 115.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cyclodipeptide synthase


Mass: 31352.633 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fluoribacter dumoffii NY 23 (bacteria) / Gene: Ldum_1689 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W0T5C6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 278 K / Method: evaporation / pH: 7.5 / Details: 11% PEG3350, 0.1M Hepes pH7.5, L-proline 0.2M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2016
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.058→190.6 Å / Num. obs: 64644 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 92.98 Å2 / CC1/2: 0.998 / Rsym value: 0.065 / Net I/σ(I): 12.65
Reflection shellResolution: 3.06→3.24 Å / Redundancy: 3.74 % / Mean I/σ(I) obs: 2.48 / Num. unique obs: 10162 / CC1/2: 0.954 / Rsym value: 0.401 / % possible all: 97.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MLQ

5mlq


Resolution: 3.06→48.16 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.868 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.397
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3212 5.02 %RANDOM
Rwork0.21 ---
obs0.212 64016 99.3 %-
Displacement parametersBiso mean: 94.59 Å2
Baniso -1Baniso -2Baniso -3
1--6.0712 Å20 Å24.9823 Å2
2---37.3795 Å20 Å2
3---43.4507 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: 1 / Resolution: 3.06→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18765 0 0 56 18821
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0119261HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1226061HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6786SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes522HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2741HARMONIC5
X-RAY DIFFRACTIONt_it19261HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion21.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2441SEMIHARMONIC5
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_contact21815SEMIHARMONIC4
LS refinement shellResolution: 3.06→3.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3709 241 5.15 %
Rwork0.2819 4439 -
all0.2864 4680 -
obs--99.38 %

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