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- PDB-8eyz: Engineered glutamine binding protein bound to GLN and a cobaloxim... -

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Basic information

Entry
Database: PDB / ID: 8eyz
TitleEngineered glutamine binding protein bound to GLN and a cobaloxime ligand
ComponentsAmino acid ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / Artificial Metalloprotein / Glutamine-binding protein / Conformationally Switchable Artificial Metallorprotein / cobaloxime ligand
Function / homology
Function and homology information


amino acid transport / ligand-gated monoatomic ion channel activity / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Glutamine-binding periplasmic protein GlnH, type 2 periplasmic binding protein fold / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins.
Similarity search - Domain/homology
GLUTAMINE / Chem-X5Z / Amino acid ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsBridwell-Rabb, J. / Boggs, D.G. / Olshansky, L. / Fatima, S. / Thompson, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138138 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Engineering a Conformationally Switchable Artificial Metalloprotein.
Authors: Fatima, S. / Boggs, D.G. / Ali, N. / Thompson, P.J. / Thielges, M.C. / Bridwell-Rabb, J. / Olshansky, L.
History
DepositionOct 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amino acid ABC transporter substrate-binding protein
B: Amino acid ABC transporter substrate-binding protein
C: Amino acid ABC transporter substrate-binding protein
D: Amino acid ABC transporter substrate-binding protein
E: Amino acid ABC transporter substrate-binding protein
F: Amino acid ABC transporter substrate-binding protein
G: Amino acid ABC transporter substrate-binding protein
H: Amino acid ABC transporter substrate-binding protein
I: Amino acid ABC transporter substrate-binding protein
J: Amino acid ABC transporter substrate-binding protein
K: Amino acid ABC transporter substrate-binding protein
L: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,11447
Polymers303,05612
Non-polymers8,05835
Water1,56787
1
A: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0315
Polymers25,2551
Non-polymers7774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9354
Polymers25,2551
Non-polymers6813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9354
Polymers25,2551
Non-polymers6813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0235
Polymers25,2551
Non-polymers7694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8393
Polymers25,2551
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9314
Polymers25,2551
Non-polymers6773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1276
Polymers25,2551
Non-polymers8735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8393
Polymers25,2551
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8393
Polymers25,2551
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9354
Polymers25,2551
Non-polymers6813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8393
Polymers25,2551
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8393
Polymers25,2551
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.125, 136.091, 150.980
Angle α, β, γ (deg.)90.000, 90.160, 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

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Amino acid ABC transporter substrate-binding protein / Glutamine ABC transporter substrate-binding protein GlnH / Glutamine ABC transporter substrate- ...Glutamine ABC transporter substrate-binding protein GlnH / Glutamine ABC transporter substrate-bindnig protein / Glutamine ABC transporter / periplasmic glutamine-binding protein (TC 3.A.1.3.2) / substrate-binding protein / Glutamine-binding periplasmic protein / Periplasmic glutamine-binding protein / Periplasmic glutamine-binding protein permease / Permease of periplasmic glutamine-binding protein


Mass: 25254.658 Da / Num. of mol.: 12 / Mutation: K23I, T72C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: glnH, A5U30_004091, A6592_04880, A8499_000176, A9X72_16950, AAG43_003583, ACN68_16860, ACN81_02400, ACU57_05845, AF998_000125, AM464_21485, APX88_17575, AT335_000554, AT845_002764, AW118_24500, ...Gene: glnH, A5U30_004091, A6592_04880, A8499_000176, A9X72_16950, AAG43_003583, ACN68_16860, ACN81_02400, ACU57_05845, AF998_000125, AM464_21485, APX88_17575, AT335_000554, AT845_002764, AW118_24500, AW119_03915, AWP47_29145, B6R12_003536, B6R15_002883, B6R31_003222, B6R48_003973, B6R87_003886, BANRA_01322, BANRA_01764, BEA19_14205, BER14_07540, BF481_003043, BG944_004267, BGM66_000966, BHS81_04935, BJI68_11495, BJJ90_17825, BK292_21345, BK383_19105, BLM69_000575, BMC79_000611, BMT49_05685, BMT50_00560, BMT91_20520, BN17_06101, BO068_000746, BOH76_16995, BON63_24725, BON64_24190, BON65_04740, BON66_07455, BON67_25290, BON68_02720, BON69_08400, BON70_24775, BON71_14305, BON72_22420, BON73_01195, BON74_14830, BON75_15470, BON76_25420, BON77_09375, BON78_20655, BON79_20060, BON80_12630, BON81_19085, BON82_15305, BON83_05500, BON84_13940, BON86_21740, BON87_16800, BON88_07465, BON89_22820, BON90_14295, BON91_21900, BON92_22285, BON93_04225, BON94_25770, BON95_05775, BON96_27115, BON97_10525, BON98_19710, BR158_002878, BRV02_000648, BSR05_11095, BTB68_001717, BTQ06_26205, BUO55_004168, BvCmsF30A_02312, BvCmsHHP019_04964, BvCmsKKP061_03133, BvCmsKSNP073_02686, BVL39_24445, BXT93_09325, BZL69_00955, C0P57_004641, C1Q91_004053, C2121_002453, C2M16_01565, C2R31_002978, C2U48_05980, C3F40_08525, C5N07_02720, C5Y87_11455, C9114_21285, C9160_24490, C9E67_21255, C9Z68_13890, CA593_25060, CCS08_19690, CCV12_002704, CDC27_03365, CDL36_05995, CDL37_06170, CF22_003152, CG831_000699, CHM61_001352, CIG67_24135, CO706_26845, CQ986_002219, CR538_17365, CR539_08495, CR628_003110, CTR35_001347, CV83915_00768, CWS33_06680, CX938_000617, CXJ73_000498, CY655_04230, D0X26_05085, D1912_20655, D1H34_001169, D3822_09995, D3C88_05045, D3G36_03255, D3Y67_17015, D4N09_12520, D4U49_00030, D9D43_04855, D9D77_09815, D9E34_09280, D9E49_16110, D9H94_11690, D9J03_11000, D9J61_05355, DAH17_03825, DAH18_19240, DAH19_07490, DAH20_21020, DAH21_16625, DAH22_20195, DAH23_12545, DAH24_12625, DAH25_13880, DAH26_12570, DAH27_27195, DAH28_26570, DAH29_21215, DAH30_24830, DAH31_23660, DAH32_25755, DAH33_16740, DAH34_00565, DAH35_19590, DAH36_01785, DAH37_00035, DAH38_23920, DAH40_16855, DAH41_26115, DAH42_14420, DAH43_13740, DAH45_14115, DAH46_16030, DAH47_10645, DAH48_08930, DAH49_15255, DAH50_02775, DD762_19985, DEN86_16580, DEN87_25365, DEN88_18460, DEN89_18240, DEN90_15895, DEN91_18520, DEN92_25370, DEN93_25685, DEN94_25170, DEN95_25645, DEN96_14460, DEN97_05945, DEN98_14610, DEN99_03305, DEO00_15605, DEO01_16930, DEO02_15845, DEO03_02745, DEO04_17445, DEO05_17315, DEO06_16065, DEO07_16850, DEO08_10875, DEO09_17170, DEO10_17430, DEO11_17320, DEO12_17235, DEO13_25310, DEO14_25015, DEO15_18570, DEO17_18420, DEO18_14095, DEO19_25855, DEO20_09480, DIV22_24420, DKP82_24310, DM870_16080, DN627_03140, DNX30_21735, DRW19_18320, DS732_09030, DTL43_10730, DTL90_03445, DTM45_05760, DU321_00670, DXT69_17235, DXT70_03865, DXT71_08710, DXT73_10050, E0I42_20880, E2112_02675, E2113_01945, E2114_18730, E2115_17055, E2116_04330, E2117_24095, E2118_16300, E2119_12420, E2120_04215, E2121_18185, E2122_15175, E2123_15570, E2124_10840, E2125_18565, E2127_00470, E2128_04955, E2129_10405, E2130_05520, E2131_16230, E2132_01450, E2133_04840, E2134_04965, E2135_16085, E2136_14980, E2646_20010, E3O05_01530, E4K51_02810, E4T14_00550, E4T84_17465, E5H86_25390, E5M02_22525, E5P22_03440, E5P23_09650, E5P24_07820, E5P25_14380, E5P26_02375, E5P27_03730, E5P28_05135, E5P29_02255, E5P30_11875, E5P31_05030, E5P32_00405, E5P33_13470, E5P34_03095, E5P35_02485, E5P36_15665, E5P37_20315, E5P39_19970, E5P40_02695, E5P41_16665, E5P42_12050, E5P43_17005, E5P44_18530, E5P45_22380, E5P46_16045, E5P47_19935, E5P48_15405, E5P49_19430, E5P50_22740, E5P51_16920, E5S34_18760, E5S35_18835, E5S36_04930, E5S37_23235, E5S38_16415, E5S39_18510, E5S43_19010, E5S44_19440, E5S45_23380, E5S46_22040, E5S47_18610, E5S48_18775, E5S51_14615, E5S52_10650, E5S53_16880, E5S54_25355, E5S55_16870, E5S56_20090, E5S57_09335, E5S58_12745, E5S61_14780, E5S62_04320, E6C80_01100, E6D34_16620, EA239_02055, EA435_03075, EAI46_17535, EAN77_08520, EAX79_16230, EC1094V2_3069, EC95NR1_05084, ECs0889, ED648_06680, EHD79_17160, EI021_00555, EIA08_01310, EIZ93_04910, EKI52_06410, EL79_3071, EL80_3032, ELT16_02415, ELT17_17330, ELT20_02820, ELT21_01480, ELT22_07560, ELT23_02015, ELT24_02785, ELT25_04925, ELT26_09185, ELT27_07495, ELT28_15430, ELT29_09190, ELT30_04155, ELT31_02235, ELT32_01320, ELT33_01125, ELT34_02155, ELT35_01150, ELT36_07860, ELT38_02015, ELT39_12720, ELT40_06625, ELT41_10995, ELT44_00485, ELT45_07655, ELT46_05645, ELT48_02765, ELT49_11575, ELT50_00370, ELT51_04720, ELT52_01735, ELT54_03790, ELT55_02630, ELT56_04370, ELT58_13405, ELT59_01975, ELT60_02685, ELT61_00525, ELT63_00400, ELT72_09395, ELU07_01290, ELU82_01275, ELU83_00030, ELU85_01090, ELU88_02755, ELU89_06090, ELU90_16660, ELU91_09660, ELU94_20245, ELU95_04135, ELU96_01710, ELU97_02075, ELU98_07325, ELU99_17975, ELV00_00990, ELV01_02685, ELV02_04500, ELV03_02685, ELV04_09130, ELV05_01070, ELV07_02685, ELV08_05490, ELV09_09705, ELV10_03635, ELV11_00495, ELV12_17700, ELV13_05135, ELV15_08005, ELV16_06920, ELV20_01690, ELV21_07280, ELV22_03390, ELV23_04940, ELV26_19830, ELV28_13395, ELV29_14030, ELV40_13070, ELX48_20960, ELX61_08885, ELX66_13645, ELX68_03535, ELX69_04805, ELX76_06605, ELX79_08650, ELX85_04825, ELX96_24945, ELY02_21695, ELY32_15660, ELY36_07870, ELY39_10000, ELY41_22740, ELY48_10875, EN85_004581, ERS085406_04011, ERS139208_02685, EWK56_11475, ExPECSC038_02876, EXX13_17615, EYV17_11920, EYV18_03835, F0L67_04275, F2N20_02135, F2N31_03410, F3N40_12265, F7F11_11485, F7N46_08470, F9413_07780, F9461_01305, F9B07_02710, F9S83_08475, F9V24_04485, F9X20_12650, FDM60_08540, FE584_14605, FE587_14715, FEJ01_13600, FFF58_04660, FGG80_18845, FHO90_02740, FHQ91_05095, FIJ20_11900, FJQ40_17745, FJQ51_03360, FJQ53_08590, FKO60_07285, FOI11_009340, FOI11_10705, FPI65_04950, FPJ29_13820, FPS11_01585, FQF29_02765, FV293_02200, FVB16_07150, FWK02_14955, FY127_05225, FZC17_24290, FZN31_16475, FZU14_07000, G3813_001838, G3V95_03410, G3W53_12740, G4A38_09725, G4A47_02555, G5603_02180, G7630_000206, G9448_06715, GAI66_11760, GAI89_13630, GAJ12_17235, GAJ26_02185, GF147_05165, GF699_09700, GFY34_01840, GIB53_03185, GJ11_04510, GJO56_05855, GKF66_09425, GKF89_13835, GNW61_02415, GNZ05_09120, GOP25_10140, GP711_00870, GP944_02795, GP965_17210, GP979_15650, GQM04_08380, GQM13_17840, GQM21_08920, GQN34_06325, GQW07_06480, GQW68_09320, GQW80_16390, GRC73_03245, GRO95_00200, GRW05_01550, GRW24_15895, GRW56_11730, GRW57_13110, GSM54_17415, GSY44_21500, GTP88_11170, GUC01_03260, GUI33_12255, H0O37_11575, H0O39_10830, H0O72_02630, HEP30_007075, HEP34_000682, HHH44_004674, HI055_001651, HIE29_000308, HIN64_003897, HJQ60_003183, HJU54_001291, HKA49_004171, HL563_07185, HL601_10425, HLV18_05320, HLX92_21635, HLZ50_00225, HmCms169_02183, HMJ82_04430, HMV95_02550, HMW38_01730, HNC36_00575, HNC59_02155, HNC66_13445, HNC99_06490, HND12_01310, HV109_16015, HV209_04855, HVV39_21020, HVW04_06960, HVW19_18030, HVW43_08305, HVY77_17775, HVZ71_16640, HX136_17495, I6H00_09980, I6H01_21610, I6H02_22350, IA00_002027, IFB95_003951, IH768_00950, IH772_11995, IT029_003785, J0541_000988, J4S20_005071, J5U05_002124, JE86ST02C_09210, JE86ST05C_09750, JFD_02409, JNP96_08670, NCTC10082_05067, NCTC10089_03418, NCTC10090_00382, NCTC10418_05048, NCTC10429_05756, NCTC10865_04252, NCTC11181_00607, NCTC12950_03687, NCTC13127_04610, NCTC13216_03355, NCTC4450_03842, NCTC7922_06781, NCTC7927_03810, NCTC7928_05513, NCTC8008_02951, NCTC8009_06196, NCTC8179_02263, NCTC8333_03962, NCTC8450_01827, NCTC8500_03700, NCTC8621_03555, NCTC8959_00379, NCTC8960_00488, NCTC9001_01370, NCTC9036_03440, NCTC9037_03540, NCTC9075_04560, NCTC9111_03455, NCTC9702_03882, NCTC9706_00702, NCTC9775_01675, NCTC9777_03409, NCTC9962_02368, ND22_002874, RG28_00455, SAMEA3472044_00248, SAMEA3472056_00231, SAMEA3472147_02754, SAMEA3751407_00314, SAMEA3752557_02233, SAMEA3753106_00906, TUM18780_29030, WP4S18E07_30170, WR15_25350, XU56_002013
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3THM2

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Non-polymers , 5 types, 122 molecules

#2: Chemical
ChemComp-X5Z / AZIDOBIS (DIMETHYLGLYOXIMATO) PYRIDINECOBALT


Mass: 438.328 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C15H23CoN8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Tris (pH=7.5), 0.2 M Ammonium Sulfate, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 61098 / % possible obs: 99.6 % / Redundancy: 3.79 % / Biso Wilson estimate: 69.72 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.14 / Net I/σ(I): 8.86
Reflection shellResolution: 2.99→3.17 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 9748 / CC1/2: 0.693 / Rrim(I) all: 0.901 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDN

1wdn


Resolution: 2.99→41.9 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.5656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2655 6119 10.02 %
Rwork0.2326 54925 -
obs0.2359 61044 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.58 Å2
Refinement stepCycle: LAST / Resolution: 2.99→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20776 0 406 87 21269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005121548
X-RAY DIFFRACTIONf_angle_d0.893529159
X-RAY DIFFRACTIONf_chiral_restr0.06053193
X-RAY DIFFRACTIONf_plane_restr0.00433689
X-RAY DIFFRACTIONf_dihedral_angle_d11.29787954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.030.50341950.44621739X-RAY DIFFRACTION94.43
3.03-3.060.41022030.35721795X-RAY DIFFRACTION99.8
3.06-3.10.41691990.35471832X-RAY DIFFRACTION99.95
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