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- PDB-7wuo: Unravelling structure of riboflavin synthase for designing of pot... -

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Basic information

Entry
Database: PDB / ID: 7wuo
TitleUnravelling structure of riboflavin synthase for designing of potential anti-bacterial drug
ComponentsRiboflavin synthase
KeywordsANTIMICROBIAL PROTEIN / riboflavin / antibacterial
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity
Similarity search - Function
Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / ATP synthase subunit alpha, N-terminal domain-like superfamily / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Riboflavin synthase
Similarity search - Component
Biological speciesLeptospira kmetyi serovar Malaysia str. Bejo-Iso9 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å
AuthorsAris, S.N.A.M. / Leow, A.T.C. / Motomura, T. / Jonet, M.A.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Ministry of Science, Technology and Innovation (MOSTI, Malaysia)02-01-04-SF1321 Malaysia
CitationJournal: J.Mol.Struct. / Year: 2022
Title: Unraveling the crystal structure of Leptospira kmetyi riboflavin synthase and computational analyses for potential development of new antibacterials
Authors: Aris, S.N.A.M. / Rahman, R.N.Z.R.A. / Ali, M.S.M. / Jonet, M.A. / Motomura, T. / Noor, N.D.M. / Shariff, F.M. / Hsu, K.C. / Chor, L.T.
History
DepositionFeb 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Riboflavin synthase
B: Riboflavin synthase
C: Riboflavin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8945
Polymers69,6823
Non-polymers2122
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-37 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.559, 130.632, 202.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 201 / Label seq-ID: 1 - 201

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Riboflavin synthase


Mass: 23227.416 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira kmetyi serovar Malaysia str. Bejo-Iso9 (bacteria)
Gene: EHQ67_13285 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7I0ICZ8, riboflavin synthase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsThe ligand should be polyethyleneglycol, because polyethyleneglycol has been used in both ...The ligand should be polyethyleneglycol, because polyethyleneglycol has been used in both crystallization formulation and as a cryoprotectant.

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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: 2.94 Å3/Da / Density % sol: 58.24 % / Description: Bullet shape
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium Sulfate, 0.1M MES monohydrate (pH 6.5), 10% w/v PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: PIXEL / Date: Apr 19, 2019 / Details: dextris 200k
RadiationMonochromator: cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.19→40 Å / Num. obs: 13224 / % possible obs: 97.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.2
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1259 / CC1/2: 0.818 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000v714ndata reduction
HKL-3000v714ndata scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I8D

1i8d


Resolution: 3.19→27.26 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.844 / SU B: 24.531 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.526
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 636 4.8 %RANDOM
Rwork0.2182 ---
obs0.2204 12554 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.34 Å2 / Biso mean: 39.875 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---2.54 Å2-0 Å2
3---2.22 Å2
Refinement stepCycle: final / Resolution: 3.19→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 14 27 4645
Biso mean--39.99 15.07 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134688
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174392
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.6436349
X-RAY DIFFRACTIONr_angle_other_deg1.2511.57310168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1935600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41522.591220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41815810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8361528
X-RAY DIFFRACTIONr_chiral_restr0.0690.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02953
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A55120.15
12B55120.15
21A54460.17
22C54460.17
31B53120.17
32C53120.17
LS refinement shellResolution: 3.193→3.275 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 44 -
Rwork0.258 949 -
all-993 -
obs--99 %

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