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- PDB-5mlq: Structure of CDPS from Nocardia brasiliensis -

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Basic information

Entry
Database: PDB / ID: 5mlq
TitleStructure of CDPS from Nocardia brasiliensis
ComponentsCDPS
KeywordsLIGASE / Cyclodipeptide Synthase
Function / homologyCyclodipeptide synthase superfamily / Cyclodipeptide synthase / Cyclodipeptide synthase / aminoacyltransferase activity / CITRIC ACID / Cyclodipeptide synthase
Function and homology information
Biological speciesNocardia brasiliensis ATCC 700358 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.18 Å
AuthorsBourgeois, G. / Seguin, J. / Moutiez, M. / Babin, M. / Belin, P. / Mechulam, Y. / Gondry, M. / Schmitt, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0021 France
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
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDPS
B: CDPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6885
Polymers57,1112
Non-polymers5763
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint0 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.287, 144.287, 103.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CDPS


Mass: 28555.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia brasiliensis ATCC 700358 (bacteria)
Gene: O3I_025450 / Production host: Escherichia coli (E. coli) / References: UniProt: K0F6G5
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7

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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: 4.74 Å3/Da / Density % sol: 74.05 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350 22% Tri-ammonium citrate 0.2M pH = 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2015
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.18→46.15 Å / Num. obs: 18802 / % possible obs: 99.5 % / Redundancy: 12.9 % / Biso Wilson estimate: 128.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 19.04
Reflection shellResolution: 3.18→3.37 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 2.05 / CC1/2: 0.846 / Rsym value: 1.25 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.18→46.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.508 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.501 / SU Rfree Blow DPI: 0.268 / SU Rfree Cruickshank DPI: 0.273
RfactorNum. reflection% reflectionSelection details
Rfree0.194 958 5.1 %RANDOM
Rwork0.168 ---
obs0.169 18800 99.4 %-
Displacement parametersBiso mean: 121.24 Å2
Baniso -1Baniso -2Baniso -3
1-17.1996 Å20 Å20 Å2
2--17.1996 Å20 Å2
3----34.3992 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 3.18→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 39 0 3681
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013760HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.135105HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1323SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes565HARMONIC5
X-RAY DIFFRACTIONt_it3760HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion20.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion486SEMIHARMONIC5
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_contact4262SEMIHARMONIC4
LS refinement shellResolution: 3.18→3.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.279 153 5.3 %
Rwork0.254 2735 -
all0.255 2888 -
obs--96.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5666-0.12381.15321.0882-0.18912.5982-0.1884-0.48950.44590.2401-0.058-0.1306-0.4748-0.2880.2464-0.06710.0244-0.0041-0.0095-0.1139-0.068960.21833.896229.7598
21.7153-0.60480.37832.28220.26081.6990.00040.0212-0.0339-0.1284-0.1010.1436-0.0003-0.21370.1006-0.13360.00920.0427-0.0223-0.0084-0.060644.550722.60794.0256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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