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- PDB-7v09: Crystal structure of ECL_RS08780, putative sugar transport system... -

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Basic information

Entry
Database: PDB / ID: 7v09
TitleCrystal structure of ECL_RS08780, putative sugar transport system periplasmic sugar-binding protein
ComponentsMultiple sugar transport system periplasmic sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / SOLUTE-BINDING PROTEIN / ALPHA/BETA DOMAIN / structural genomics / CSGID / center for structural genomics of infectious diseases / NIAID / national institute of allergy and infectious diseases
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / outer membrane-bounded periplasmic space / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Multiple sugar transport system periplasmic sugar-binding protein
Function and homology information
Biological speciesEnterobacter cloacae subsp. cloacae ATCC 13047 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStogios, P.J. / Skarina, T. / Mesa, N. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of ECL_RS08780, putative sugar transport system periplasmic sugar-binding protein
Authors: Stogios, P.J.
History
DepositionMay 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multiple sugar transport system periplasmic sugar-binding protein
B: Multiple sugar transport system periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9197
Polymers89,7972
Non-polymers1225
Water9,728540
1
A: Multiple sugar transport system periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9714
Polymers44,8991
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multiple sugar transport system periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9473
Polymers44,8991
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.956, 67.618, 86.656
Angle α, β, γ (deg.)90.000, 104.220, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Multiple sugar transport system periplasmic sugar-binding protein


Mass: 44898.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae ATCC 13047 (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56
Gene: ECL_01781 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A0H3CHG3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.86 Å / Num. obs: 51868 / % possible obs: 97.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.066 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3675 / CC1/2: 0.624 / Rpim(I) all: 0.373 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2→19.86 Å / SU ML: 0.2731 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.0261
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2956 2508 4.91 %RANDOM
Rwork0.2501 48587 --
obs0.2523 51095 96.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.56 Å2
Refinement stepCycle: LAST / Resolution: 2→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 0 5 540 6745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196328
X-RAY DIFFRACTIONf_angle_d0.4488600
X-RAY DIFFRACTIONf_chiral_restr0.0412989
X-RAY DIFFRACTIONf_plane_restr0.00341112
X-RAY DIFFRACTIONf_dihedral_angle_d15.86962300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.38781400.31922592X-RAY DIFFRACTION93.59
2.04-2.080.29561610.29442661X-RAY DIFFRACTION96.31
2.08-2.130.35381430.28822657X-RAY DIFFRACTION95.92
2.13-2.170.30851440.29192696X-RAY DIFFRACTION96.14
2.17-2.230.5051060.41732325X-RAY DIFFRACTION83.54
2.23-2.290.64071110.52712348X-RAY DIFFRACTION83.75
2.29-2.360.32961520.29082714X-RAY DIFFRACTION97.32
2.36-2.430.33251290.27372764X-RAY DIFFRACTION97.9
2.43-2.520.31271490.26172717X-RAY DIFFRACTION98.15
2.52-2.620.29731680.2622750X-RAY DIFFRACTION98.51
2.62-2.740.32531490.25052731X-RAY DIFFRACTION98.66
2.74-2.880.30671520.24692770X-RAY DIFFRACTION98.92
2.88-3.060.28511230.24072795X-RAY DIFFRACTION98.68
3.06-3.30.28111310.2342779X-RAY DIFFRACTION99.01
3.3-3.630.27511450.22182799X-RAY DIFFRACTION98.99
3.63-4.150.2661420.21452759X-RAY DIFFRACTION97.91
4.15-5.210.20741310.17932848X-RAY DIFFRACTION99.63
5.21-19.860.2011320.19222882X-RAY DIFFRACTION99.08
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)
12.62422434063-0.1668947991472.867363057185.410893001351.465413128613.56516818553-0.198377419613-0.4936524269550.4947897354760.5363902958880.121268762332-0.153054461343-0.244640380883-0.2547650643530.04241534814390.2657307758560.03559764803230.03639181481490.236593323884-0.08418302110820.36757396683713.64165129923.544596021827.6872300756
20.9485042932330.219467195457-0.03073148803572.45502200048-0.03275301365530.63389083480.0518489154442-0.0284030903099-0.01627080602790.17004874471-0.0447342898622-0.185875759786-0.02751007046730.0159733207073-0.006001783294090.119967730204-0.00829523850056-0.04096602178290.171418176176-0.02165642083310.28481927815417.8891242017-1.7181389299220.3801418467
30.5373432915340.177125508242-0.2845372099082.280777955490.5985437679210.7116728433040.0722359618037-0.0884567964732-0.08104867849330.2972715539160.0802960379123-0.308573697038-0.04750534766630.239036802132-0.1577655637490.195494015063-0.0193957301018-0.07915013727540.183622693621-0.02082967625960.27461749603823.7961034854.5276163162825.819753213
45.707745302692.67810681387-2.693981617243.967378769811.347518920487.443698574710.08981616773260.191262685592-0.155496674838-0.2169841087250.2832276421250.195228430693-0.2344982611690.101963664163-0.354755054320.110188122870.00472992541018-0.04338583383450.204256851455-0.04330104872330.2889825438997.47525275891-14.33446388656.62580066883
52.953774564370.649353740935-3.006814312824.40419931912-1.853048840244.045606518440.00260468802362-0.660508842367-0.6955790288680.52026275455-0.0362194231443-0.08242395480640.3176734077780.425777593459-0.005040793630870.3076890719580.0212851512305-0.07093394727590.2993790603880.1312792880780.407443821167-13.432941347-29.90650163827.9147029834
63.103759901240.571786390505-0.2698361198533.53816781437-0.3587023523692.49801039504-0.0244453583160.1973902092-0.183596865406-0.1359529408060.087646200872-0.3120230814680.1286701773160.027679235201-0.04546846864420.170310175315-0.022126964824-0.02054943769380.153901389813-0.0345472548770.369341736821-12.918997334-21.850885672713.0326040025
71.555091836130.3080034924920.2018445971742.04710897371-0.6830091050750.6281670373360.0514092518575-0.1977020736950.560092996010.445368896580.05238660350240.616394147452-0.1826333826770.0392398950005-0.06301227085820.243940302535-0.04164765252250.1092557385130.224948562323-0.02709821924450.503016686235-23.63742762641.0083099939323.9618366943
81.96956021621.22587477759-0.1631835510173.33140740062-0.3196720510080.7667281191550.256052908617-0.240256699810.2200976584310.526592550325-0.211327379710.4962559512-0.106132379961-0.0222497555029-0.04061521599770.225453015831-0.03071243764760.04387173312670.196164439467-0.01406079179910.310543224585-18.9312168425-4.6382184267523.221710438
94.09259721881.772881771692.043194279721.56668688387-0.3311857965727.267328759360.0008027632894070.1545589503840.5604947406520.1398206820730.0607760782172-0.07378358580070.3701870695620.288090364957-0.03103910729890.0709426690984-0.006143252530420.008215028442950.1935206993820.08611714017550.325999553914-7.510671274488.105099565396.68513367698
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 68 )AA27 - 681 - 42
22chain 'A' and (resid 69 through 323 )AA69 - 32343 - 297
33chain 'A' and (resid 324 through 396 )AA324 - 396298 - 370
44chain 'A' and (resid 397 through 429 )AA397 - 429371 - 403
55chain 'B' and (resid 27 through 68 )BB27 - 681 - 42
66chain 'B' and (resid 69 through 117 )BB69 - 11743 - 91
77chain 'B' and (resid 118 through 183 )BB118 - 18392 - 157
88chain 'B' and (resid 184 through 396 )BB184 - 396158 - 370
99chain 'B' and (resid 397 through 429 )BB397 - 429371 - 403

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