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- PDB-5lfc: Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally... -

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Basic information

Entry
Database: PDB / ID: 5lfc
TitleCrystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated dextransucrase DSR-M
ComponentsDsrV
KeywordsTRANSFERASE / dextransucrase / dextran
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity
Similarity search - Function
Glucansucrase / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Golgi alpha-mannosidase II / Glycoside hydrolase superfamily / TIM Barrel ...Glucansucrase / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Golgi alpha-mannosidase II / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLeuconostoc citreum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsClaverie, M. / Cioci, G. / Remaud-simeon, M. / Moulis, C. / Tranier, S.
CitationJournal: Acs Catalysis / Year: 2017
Title: Investigations on the Determinants Responsible for Low Molar Mass Dextran Formation by DSR-M Dextransucrase
Authors: Claverie, M. / Cioci, G. / Vuillemin, M. / Monties, N. / Roblin, P. / Lippens, G. / Remaud-simeon, M. / Moulis, C.
History
DepositionJul 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / 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: DsrV
B: DsrV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,7986
Polymers288,5342
Non-polymers2644
Water21612
1
A: DsrV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3993
Polymers144,2671
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DsrV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3993
Polymers144,2671
Non-polymers1322
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.840, 128.710, 229.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 288 - 1436 / Label seq-ID: 128 - 1276

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein DsrV


Mass: 144266.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc citreum (bacteria) / Gene: dsrV / Plasmid: pet55 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2H4A2M1*PLUS, dextransucrase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.05 Å3/Da / Density % sol: 59.67 % / Description: thin rod
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350 20%, 0.1M BIS-TRIS pH 6.5, 0.4M KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 9, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→114.67 Å / Num. obs: 51658 / % possible obs: 98.7 % / Redundancy: 5.2 % / Rsym value: 0.15 / Net I/av σ(I): 4.858 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.2-3.374.20.4531.7198.4
3.37-3.584.20.3012.6197.8
3.58-3.8240.2013.8197.4
3.82-4.135.60.174.3198.3
4.13-4.538.10.1475199.9
4.53-5.068.10.1365.3199.9
5.06-5.844.50.1335.6199.8
5.84-7.164.50.1226.1199.5
7.16-1040.0729.8198.9
10.12-49.2334.40.04813.6198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AIB

3aib


Resolution: 3.2→114.67 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.875 / SU B: 56.923 / SU ML: 0.416 / SU R Cruickshank DPI: 0.4759 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.492
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 2531 4.9 %RANDOM
Rwork0.2213 ---
obs0.2226 49085 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.16 Å2 / Biso mean: 53.518 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å2-0 Å2
2---2.1 Å2-0 Å2
3---4.46 Å2
Refinement stepCycle: final / Resolution: 3.2→114.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18003 0 14 12 18029
Biso mean--48.55 26.83 -
Num. residues----2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218405
X-RAY DIFFRACTIONr_bond_other_d0.0030.0216581
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.93125000
X-RAY DIFFRACTIONr_angle_other_deg1.084338106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38852292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76325.623955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28152941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5261562
X-RAY DIFFRACTIONr_chiral_restr0.0680.22688
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221726
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024456
X-RAY DIFFRACTIONr_mcbond_it0.8542.8959176
X-RAY DIFFRACTIONr_mcbond_other0.8532.8959175
X-RAY DIFFRACTIONr_mcangle_it1.4114.34311460
Refine LS restraints NCS

Ens-ID: 1 / Number: 68258 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 174 -
Rwork0.312 3559 -
all-3733 -
obs--98.16 %
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)
11.18880.0167-0.08480.14420.00160.35770.05990.23850.0477-0.0598-0.03350.0184-0.0166-0.0537-0.02640.21850.0022-0.03150.06440.01120.0095-34.275613.8027-23.9151
20.4326-0.1073-0.28990.4688-0.05610.60260.0520.03590.1307-0.00520.0039-0.112-0.0771-0.1699-0.05580.41460.06010.02740.22270.02320.1957-23.7225-14.784527.4951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A288 - 2001
2X-RAY DIFFRACTION2B288 - 2001

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