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- PDB-7l9r: Crystal Structure of a putative deoxyhypusine synthase from Entam... -

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Basic information

Entry
Database: PDB / ID: 7l9r
TitleCrystal Structure of a putative deoxyhypusine synthase from Entamoeba histolytica
ComponentsDeoxyhypusine synthase, putative
KeywordsTRANSFERASE / SSGCID / putative deoxyhypusine synthase / Entamoeba histolytica / EHI_098350 / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologypeptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily / cytoplasm / Deoxyhypusine synthase, putative
Function and homology information
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a putative deoxyhypusine synthase from Entamoeba histolytica
Authors: Abendroth, J. / Davies, D.R. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: 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: Deoxyhypusine synthase, putative
B: Deoxyhypusine synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1734
Polymers79,1022
Non-polymers712
Water3,063170
1
A: Deoxyhypusine synthase, putative
B: Deoxyhypusine synthase, putative
hetero molecules

A: Deoxyhypusine synthase, putative
B: Deoxyhypusine synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,3468
Polymers158,2054
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area10850 Å2
ΔGint-100 kcal/mol
Surface area45660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.900, 85.900, 424.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

21B-534-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 34 or resid 36...
d_2ens_1(chain "B" and (resid 5 through 11 or (resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILEGLYA1 - 30
d_12ens_1ALASERA32 - 45
d_13ens_1GLUMETA47 - 72
d_14ens_1THRPHEA74 - 81
d_15ens_1TYRLEUA83 - 84
d_16ens_1GLUILEA86 - 119
d_17ens_1LYSTHRA121 - 150
d_18ens_1METTHRA152 - 179
d_19ens_1GLYLEUA181 - 206
d_110ens_1LEULEUA208 - 256
d_111ens_1PHEILEA258 - 276
d_21ens_1ILEGLYC1 - 30
d_22ens_1ALASERC32 - 45
d_23ens_1GLUMETC47 - 72
d_24ens_1THRPHEC74 - 81
d_25ens_1TYRLEUC83 - 84
d_26ens_1GLUILEC86 - 119
d_27ens_1LYSTHRC121 - 150
d_28ens_1METTHRC152 - 179
d_29ens_1GLYLEUC181 - 206
d_210ens_1LEUHISC208 - 231
d_211ens_1GLULEUC242 - 266
d_212ens_1PHEILEC268 - 286

NCS oper: (Code: givenMatrix: (-0.999284008335, -0.00977665270541, 0.0365497981995), (-0.00156085801541, 0.975867275561, 0.218358934352), (-0.0378025714576, 0.21814554213, -0.975183822692)Vector: 33. ...NCS oper: (Code: given
Matrix: (-0.999284008335, -0.00977665270541, 0.0365497981995), (-0.00156085801541, 0.975867275561, 0.218358934352), (-0.0378025714576, 0.21814554213, -0.975183822692)
Vector: 33.249474307, -0.223713844967, 0.712004538044)

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Components

#1: Protein Deoxyhypusine synthase, putative


Mass: 39551.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_098350 / Plasmid: EnhiA.00933.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C4LXB8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Microlytic MCSG1 screen, condition F3: 200mM ammonium citrate dibasic pH 5, 20% (w/V) PEG 3350: EnhiA.00933.a.A1.PW26259 at 25.43mg/ml + 4mM NAD + 4mM GC7 (Deoxyhypusine Synthase Inhibitor) : ...Details: Microlytic MCSG1 screen, condition F3: 200mM ammonium citrate dibasic pH 5, 20% (w/V) PEG 3350: EnhiA.00933.a.A1.PW26259 at 25.43mg/ml + 4mM NAD + 4mM GC7 (Deoxyhypusine Synthase Inhibitor) : tray 314273 F3: cryo: 20% EG + compounds: puck: tds8-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 20, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 37832 / % possible obs: 99.9 % / Redundancy: 11.678 % / Biso Wilson estimate: 56.327 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.072 / Χ2: 0.931 / Net I/σ(I): 22.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.4612.2020.5743.6127050.960.598100
2.46-2.5312.0360.54.3126640.9590.522100
2.53-2.612.0910.4055.325830.9730.423100
2.6-2.6812.0440.3156.8725010.9910.328100
2.68-2.7712.0480.2358.9724520.9920.245100
2.77-2.8711.9420.19610.7823680.9940.204100
2.87-2.9811.970.15514.1422740.9950.162100
2.98-3.111.8490.12617.4222040.9960.131100
3.1-3.2411.8680.10321.0721210.9980.107100
3.24-3.3911.6760.08425.5320510.9980.087100
3.39-3.5811.580.06731.2219580.9990.07100
3.58-3.7911.610.0635.0818320.9990.063100
3.79-4.0611.4270.05140.1417580.9990.053100
4.06-4.3811.3550.04842.7916510.9990.0599.9
4.38-4.811.2720.04246.2415310.9990.044100
4.8-5.3711.2090.04145.6614020.9990.043100
5.37-6.211.0880.04144.3512540.9990.043100
6.2-7.5910.810.03847.6910800.9990.04100
7.59-10.7310.2150.03251.248970.9990.034100
10.73-508.4890.03946.455460.9990.04196

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4 4035refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: domains from PDB entries 6p4v and 3n89 as per Morda

6p4v

3n89


Resolution: 2.4→42.73 Å / SU ML: 0.2595 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 2010 5.34 %0
Rwork0.187 35655 --
obs0.1886 37665 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.89 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 2 170 4444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00444447
X-RAY DIFFRACTIONf_angle_d0.64596062
X-RAY DIFFRACTIONf_chiral_restr0.0465735
X-RAY DIFFRACTIONf_plane_restr0.0046770
X-RAY DIFFRACTIONf_dihedral_angle_d12.4821614
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.05133920349 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.27451390.22922460X-RAY DIFFRACTION99.81
2.46-2.530.2871440.22362492X-RAY DIFFRACTION99.89
2.53-2.60.2771450.22142473X-RAY DIFFRACTION99.96
2.6-2.680.28951470.23752477X-RAY DIFFRACTION100
2.68-2.780.2861340.22962486X-RAY DIFFRACTION99.92
2.78-2.890.27961510.22652486X-RAY DIFFRACTION99.89
2.89-3.020.25961220.20572508X-RAY DIFFRACTION99.92
3.02-3.180.25061510.21822532X-RAY DIFFRACTION100
3.18-3.380.25341490.21962523X-RAY DIFFRACTION100
3.38-3.640.23141380.19132540X-RAY DIFFRACTION100
3.64-4.010.19941300.1622583X-RAY DIFFRACTION100
4.01-4.590.17151450.14862599X-RAY DIFFRACTION100
4.59-5.780.17451530.16762652X-RAY DIFFRACTION100
5.78-42.730.19631620.17992844X-RAY DIFFRACTION99.5
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)
10.239743355313-0.0588048216717-0.01090545871442.451669407291.522846885683.598216519-0.05223837620260.02899039120660.0821686148486-0.135736679764-0.2594870438290.3708123974490.0213706848755-0.6226311828270.268442729770.3307129375030.0216759533818-0.04045894194850.435196859117-0.09660841983490.3826060040537.34585005781-14.347991850620.1854744825
23.62710735146-0.008845165321420.05753529321242.363848285370.6243569236634.653444851720.02014308621210.115406291075-0.3421730178340.02105493753120.00847875748876-0.1537663284911.051579627250.427414672383-0.03249694396920.6670094634640.1732709204510.009383932643770.321929342119-0.02105220621260.38615659447623.1733518704-31.79761089297.87170526345
34.47926880963.359364324330.08886707583437.01244218833-0.710426847845.08186012785-0.3284739666080.1056132446450.00155014144261-0.462776001151-0.03791542526590.1988290323560.00851089924919-0.907711542380.3380085285470.3214607967420.0866241413169-0.0389906944520.470982997435-0.1873535059520.4241925652684.87585409767-15.227937155215.4815021897
40.1856949417110.0036215838070.3137657652594.16878456832-2.294954861812.315735060090.04390790899180.0488333322835-0.0116364282070.0055014548666-0.343327927227-0.612516302850.03430595292130.6400126463090.1657179024570.3317526140860.06011749486770.05564696526880.5081407381360.01276181219260.42418591158527.1283825941-9.84838256694-22.5209764337
56.047934855420.4699587650612.095972038762.43723124236-0.9416225960895.257731033840.106864357866-0.221516942125-0.478958110512-0.2419736999060.1061080905430.04851265802071.10896555164-0.301174335243-0.1438548691960.644281310161-0.06982671507550.01449142422930.289130286989-0.03591152485540.40674210883110.4405049131-29.3880702861-14.8291150585
65.20047715318-1.76328055958-0.0820061562197.467316870060.7016274583214.80891973739-0.527763905119-0.234070930962-0.1330341691340.686909491282-0.141662694973-0.7351648016310.1138306542331.20657798960.4475405277530.3692348140290.02139399178860.03223470582260.5647227111650.156261602680.55667105625330.0519933852-12.6033331714-16.0702564174
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 102 )AA5 - 1021 - 98
22chain 'A' and (resid 103 through 237 )AA103 - 23799 - 214
33chain 'A' and (resid 238 through 331 )AA238 - 331215 - 276
44chain 'B' and (resid 5 through 102 )BC5 - 1021 - 98
55chain 'B' and (resid 103 through 237 )BC103 - 23799 - 214
66chain 'B' and (resid 238 through 331 )BC238 - 331215 - 286

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