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- PDB-6jil: Crystal structure of D-cycloserine synthetase DcsG -

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Basic information

Entry
Database: PDB / ID: 6jil
TitleCrystal structure of D-cycloserine synthetase DcsG
ComponentsCycloserine biosynthesis protein DcsG
KeywordsLIGASE / ATP-grasp family / antibiotic / biosynthesis
Function / homology
Function and homology information


O-ureido-D-serine cyclo-ligase / cyclo-ligase activity / antibiotic biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / L(+)-TARTARIC ACID / Cycloserine biosynthesis protein DcsG
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsMatoba, Y. / Sugiyama, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K07997 Japan
CitationJournal: Febs J. / Year: 2020
Title: Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis.
Authors: Matoba, Y. / Uda, N. / Kudo, M. / Sugiyama, M.
History
DepositionFeb 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cycloserine biosynthesis protein DcsG
B: Cycloserine biosynthesis protein DcsG
C: Cycloserine biosynthesis protein DcsG
D: Cycloserine biosynthesis protein DcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,32027
Polymers136,8914
Non-polymers3,42823
Water13,619756
1
A: Cycloserine biosynthesis protein DcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9996
Polymers34,2231
Non-polymers7765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-12 kcal/mol
Surface area12740 Å2
MethodPISA
2
B: Cycloserine biosynthesis protein DcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1497
Polymers34,2231
Non-polymers9266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-15 kcal/mol
Surface area12660 Å2
MethodPISA
3
C: Cycloserine biosynthesis protein DcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1497
Polymers34,2231
Non-polymers9266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-11 kcal/mol
Surface area12850 Å2
MethodPISA
4
D: Cycloserine biosynthesis protein DcsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0237
Polymers34,2231
Non-polymers8006
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-25 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.450, 120.730, 102.810
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cycloserine biosynthesis protein DcsG


Mass: 34222.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: dcsG / Plasmid: pET-dcsG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D2Z030, O-ureido-D-serine cyclo-ligase
#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.0 M potassium sodium L-tartrate, 0.1 M Tris-HCl buffer (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97864 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2.32→100 Å / Num. obs: 55347 / % possible obs: 95.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.1
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 1.8 / % possible all: 82.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→29.76 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1851637.9 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2816 5.1 %RANDOM
Rwork0.195 ---
obs0.195 55347 94.6 %-
Solvent computationBsol: 41.36 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.06 Å20 Å2-4.64 Å2
2---4.56 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.32→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9184 0 217 756 10157
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 2.32→2.47 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 429 5.4 %
Rwork0.261 7545 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/PROTEIN_REP.PARAMCNS_TOPPAR/PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR/WATER_REP.PARAMCNS_TOPPAR/WATER.TOP
X-RAY DIFFRACTION3ADP.PARAMADP.TOP
X-RAY DIFFRACTION4CNS_TOPPAR/ION.PARAMCNS_TOPPAR/ION.TOP

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