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- PDB-6nlp: The crystal structure of an ABC transporter periplasmic binding p... -

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Basic information

Entry
Database: PDB / ID: 6nlp
TitleThe crystal structure of an ABC transporter periplasmic binding protein YdcS from Escherichia coli BW25113
ComponentsBacterial extracellular solute-binding family protein
KeywordsTRANSPORT PROTEIN / ABC transporter / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologypolyamine binding / polyamine transport / Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / IMIDAZOLE / Bacterial extracellular solute-binding family protein
Function and homology information
Biological speciesEscherichia coli 1-392-07_S4_C3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTan, K. / SKarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / 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: The crystal structure of an ABC transporter periplasmic binding protein YdcS from Escherichia coli BW25113
Authors: Tan, K. / SKarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A.
History
DepositionJan 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Bacterial extracellular solute-binding family protein
B: Bacterial extracellular solute-binding family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5288
Polymers81,1412
Non-polymers3866
Water7,062392
1
A: Bacterial extracellular solute-binding family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8886
Polymers40,5711
Non-polymers3175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacterial extracellular solute-binding family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6402
Polymers40,5711
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.895, 42.896, 122.771
Angle α, β, γ (deg.)90.00, 121.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacterial extracellular solute-binding family protein


Mass: 40570.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 1-392-07_S4_C3 (bacteria)
Gene: AD40_1746 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: A0A080FXI0
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M NaCl, 0.1M HEPES, 25% PEG3350, 1% Trehalose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2018 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.9→40.908 Å / Num. obs: 56396 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 18.16 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.055 / Rrim(I) all: 0.105 / Χ2: 0.759 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 2719 / CC1/2: 0.487 / Rpim(I) all: 0.516 / Rrim(I) all: 0.935 / Χ2: 0.801 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→40.908 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.16
RfactorNum. reflection% reflection
Rfree0.227 2572 4.91 %
Rwork0.1806 --
obs0.1829 52408 91.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 26 393 5950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095891
X-RAY DIFFRACTIONf_angle_d0.9268047
X-RAY DIFFRACTIONf_dihedral_angle_d6.5944684
X-RAY DIFFRACTIONf_chiral_restr0.06842
X-RAY DIFFRACTIONf_plane_restr0.0081045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93660.3068580.22871323X-RAY DIFFRACTION44
1.9366-1.97610.2858920.22191776X-RAY DIFFRACTION60
1.9761-2.01910.28281220.21672415X-RAY DIFFRACTION81
2.0191-2.0660.26441480.21332807X-RAY DIFFRACTION93
2.066-2.11770.28121620.20022869X-RAY DIFFRACTION97
2.1177-2.1750.23271520.18822901X-RAY DIFFRACTION98
2.175-2.2390.22751430.18492990X-RAY DIFFRACTION98
2.239-2.31120.27091470.19152898X-RAY DIFFRACTION97
2.3112-2.39380.25631540.18422957X-RAY DIFFRACTION98
2.3938-2.48960.22091710.18712913X-RAY DIFFRACTION99
2.4896-2.60290.22641630.18512973X-RAY DIFFRACTION99
2.6029-2.74010.261600.18933003X-RAY DIFFRACTION99
2.7401-2.91180.2541410.18592960X-RAY DIFFRACTION98
2.9118-3.13650.23211620.1922910X-RAY DIFFRACTION97
3.1365-3.4520.22581520.18693014X-RAY DIFFRACTION99
3.452-3.95120.20571430.16353042X-RAY DIFFRACTION99
3.9512-4.97670.17161390.14422981X-RAY DIFFRACTION97
4.9767-40.9170.19561630.17333104X-RAY DIFFRACTION98
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)
11.94180.0979-0.67222.4601-0.08331.9951-0.072-0.1851-0.26490.16080.0680.20690.2928-0.1930.02350.199-0.0893-0.02240.19950.07360.186967.78476.088655.6802
21.3167-0.4919-0.88681.6910.03152.16650.1258-0.07560.0120.1646-0.03230.1689-0.0829-0.149-0.06970.1041-0.0386-0.01580.12970.04240.10968.859421.538354.2272
31.7018-0.5017-0.1382.246-0.72232.12180.06380.17730.0978-0.3893-0.0755-0.13460.01710.05960.02360.18940.0094-0.05050.1260.04970.083378.04224.275829.8121
40.5951-0.1967-0.90551.336-0.09952.24940.00840.0066-0.2095-0.0406-0.03160.00220.2869-0.01640.02430.1445-0.0129-0.07190.15160.03540.139777.42412.750243.1836
50.90630.0261-0.16621.4284-0.01341.30850.066-0.07520.01040.0834-0.03390.0223-0.03890.0296-0.01480.0843-0.0527-0.06240.13650.02340.083574.155220.405150.2553
62.0701-0.6537-1.10772.12250.13063.1474-0.0016-0.25780.31030.2407-0.16620.3192-0.62240.08570.09540.1926-0.0064-0.02530.1952-0.10720.193946.102419.885321.7934
71.4533-0.2255-0.21692.43370.24672.2374-0.0736-0.1590.20490.2184-0.02040.0385-0.4035-0.17510.10670.18460.023-0.04960.1566-0.04970.171845.952818.448819.1542
81.679-0.3318-0.50782.196-0.1332.0682-0.1109-0.219-0.02250.466-0.02770.07150.0261-0.03930.09230.15620.00010.00840.1866-0.02890.091946.02953.582424.8988
91.5303-0.1912-0.86681.8421-0.5453.71980.07060.04160.0552-0.0371-0.16930.03060.19330.02050.09150.05120.0406-0.01270.1069-0.02870.110548.62633.131811.4221
102.1467-0.6446-0.03231.72140.12481.3370.01860.16120.0798-0.3319-0.1425-0.37430.03040.08990.02720.11360.07290.08160.16690.05210.253562.68055.2640.537
111.3298-0.0598-0.24951.5280.00111.3446-0.11590.03550.08440.0249-0.1415-0.0726-0.0332-0.0967-0.00510.03950.0562-0.05730.1128-0.00360.116350.68186.912411.6522
120.97670.0876-0.35791.5401-0.17221.78760.02980.05870.15480.0281-0.06250.3633-0.0693-0.4610.18050.09090.01190.00050.2099-0.09770.191836.903710.708613.645
132.6516-0.06930.35651.57850.21841.7688-0.0551-0.16610.0095-0.0121-0.0346-0.34390.2120.0660.03080.1040.0196-0.00080.11030.02620.160458.8308-1.688911.1953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 236 )
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 295 )
5X-RAY DIFFRACTION5chain 'A' and (resid 296 through 381 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 50 )
7X-RAY DIFFRACTION7chain 'B' and (resid 51 through 85 )
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 156 )
10X-RAY DIFFRACTION10chain 'B' and (resid 157 through 267 )
11X-RAY DIFFRACTION11chain 'B' and (resid 268 through 295 )
12X-RAY DIFFRACTION12chain 'B' and (resid 296 through 338 )
13X-RAY DIFFRACTION13chain 'B' and (resid 339 through 381 )

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