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- PDB-6w3z: Crystal Structure of Brugia malayi Deoxyhypusine synthase (DHPS) -

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Basic information

Entry
Database: PDB / ID: 6w3z
TitleCrystal Structure of Brugia malayi Deoxyhypusine synthase (DHPS)
ComponentsBMA-DHPS-1, isoform a
KeywordsTRANSFERASE / Brugia malayi / Deoxyhypusine synthase / Structural Genomics Consortium / SGC
Function / homologyDeoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / peptidyl-lysine modification to peptidyl-hypusine / DHS-like NAD/FAD-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / BMA-DHPS-1, isoform a
Function and homology information
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSantiago, A.S. / dos Reis, C.V. / Ramos, P.Z. / Klippel, H.A. / Silva, S.F. / Zanelli, C.F. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Counago, R.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)465651/2014-3 Brazil
Sao Paulo Research Foundation (FAPESP)2014/50897-0 Brazil
CitationJournal: Plos Negl Trop Dis / Year: 2020
Title: Structural features and development of an assay platform of the parasite target deoxyhypusine synthase of Brugia malayi and Leishmania major.
Authors: Silva, S.F. / Klippel, A.H. / Ramos, P.Z. / Santiago, A.D.S. / Valentini, S.R. / Bengtson, M.H. / Massirer, K.B. / Bilsland, E. / Counago, R.M. / Zanelli, C.F.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: BMA-DHPS-1, isoform a
B: BMA-DHPS-1, isoform a
C: BMA-DHPS-1, isoform a
D: BMA-DHPS-1, isoform a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,01113
Polymers164,5254
Non-polymers2,4869
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31410 Å2
ΔGint-185 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.753, 136.320, 75.883
Angle α, β, γ (deg.)90.000, 92.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BMA-DHPS-1, isoform a / BMA-DHPS-1 / isoform b / BMA-DHPS-1 / isoform c


Mass: 41131.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: bma-dhps-1, Bm1_16300, Bma-dhps-1, Bm14681, BM_Bm14681
Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3 / References: UniProt: A0A0J9XTC4
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 0.2M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2018
Details: Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2.3→29.42 Å / Num. obs: 62547 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.084 / Rrim(I) all: 0.155 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.363.40.881545846090.5650.5631.0481.199.7
10.29-29.413.10.03421296900.9960.0220.0416.794.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQD

1rqd


Resolution: 2.3→29.41 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.379 / SU ML: 0.21 / SU R Cruickshank DPI: 0.3769 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.377 / ESU R Free: 0.218
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 2885 4.6 %RANDOM
Rwork0.1882 ---
obs0.1894 59634 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.5 Å2 / Biso mean: 34.024 Å2 / Biso min: 17.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å21.55 Å2
2---2.53 Å2-0 Å2
3---1.74 Å2
Refinement stepCycle: final / Resolution: 2.3→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10533 0 163 397 11093
Biso mean--79.65 37.34 -
Num. residues----1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01310934
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179620
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.63614878
X-RAY DIFFRACTIONr_angle_other_deg1.2331.57522256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0851377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7822.954562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.151151670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2591559
X-RAY DIFFRACTIONr_chiral_restr0.0550.21471
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022292
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 225 -
Rwork0.297 4378 -
all-4603 -
obs--99.65 %

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