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- PDB-7xjm: Structure of VcPotD1 in complex with spermidine -

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Basic information

Entry
Database: PDB / ID: 7xjm
TitleStructure of VcPotD1 in complex with spermidine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / PotD family / polyamine binding protein / spermidine / Vibrio cholerae
Function / homologypolyamine binding / polyamine transport / Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / SPERMIDINE / Putrescine-binding periplasmic protein
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.755 Å
AuthorsMa, Q. / Liu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: structure of VcPotD1 in complex with spermidine
Authors: Ma, Q. / Liu, C.
History
DepositionApr 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putrescine-binding periplasmic protein
B: Putrescine-binding periplasmic protein
C: Putrescine-binding periplasmic protein
D: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,48811
Polymers148,1484
Non-polymers1,3407
Water14,304794
1
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4653
Polymers37,0371
Non-polymers4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1822
Polymers37,0371
Non-polymers1451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4653
Polymers37,0371
Non-polymers4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3763
Polymers37,0371
Non-polymers3392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.825, 87.214, 174.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putrescine-binding periplasmic protein


Mass: 37036.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_1424 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KS37
#2: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystal of VcPotD1 in complex with spermidine was grown in the drop containing 1.5 ul 60 mg/ml protein (10 mM HEPES, 150 mM NaCl, pH 7.5, incubated with 32.4 mM spermidine for 2 h at 4 ...Details: The crystal of VcPotD1 in complex with spermidine was grown in the drop containing 1.5 ul 60 mg/ml protein (10 mM HEPES, 150 mM NaCl, pH 7.5, incubated with 32.4 mM spermidine for 2 h at 4 oC) and 1.5 ul reservoir solution (100 mM sodium cacodylate HCl/pH 6.5, 32% PEG 8000, 200 mM sodium acetate).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.755→87.26 Å / Num. obs: 131344 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Rsym value: 0.087 / Net I/σ(I): 16.9
Reflection shellResolution: 1.755→1.761 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1255 / CC1/2: 0.779 / Rpim(I) all: 0.332 / Rrim(I) all: 1.214 / Rsym value: 1.167 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.27data extraction
XDSFeb 5, 2021, built on 20210323data reduction
Aimlessversion 0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1POY

1poy


Resolution: 1.755→87.26 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.201 6559 5 %RANDOM
Rwork0.183 ---
obs0.184 131246 99.1 %-
Displacement parametersBiso max: 130.1 Å2 / Biso mean: 37.08 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.594 Å20 Å20 Å2
2---2.3495 Å20 Å2
3---3.9434 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.755→87.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10288 0 91 794 11173
Biso mean--46.25 38.3 -
Num. residues----1281
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3660SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes281HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1478HARMONIC5
X-RAY DIFFRACTIONt_it10673HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1339SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13060SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10673HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14455HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion17.4
LS refinement shellResolution: 1.755→1.79 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.24 431 5.04 %
Rwork0.216 8122 -
obs--88.5 %
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)
11.7298-0.4950.42151.7684-0.55221.80520.0698-0.0374-0.0967-0.1088-0.06610.12140.2441-0.4286-0.0036-0.05750.0149-0.01280.0343-0.0287-0.0862-39.3546-0.3005-10.071
21.3099-0.0717-0.07421.6196-0.38691.96330.08520.38020.2137-0.1983-0.1024-0.023-0.0317-0.29480.0172-0.10230.10920.0258-0.0010.0675-0.1062-32.48828.6977-18.2869
31.39720.2727-1.47241.5023-0.29794.41230.2629-0.02740.39490.1214-0.1055-0.18-0.77740.0172-0.1574-0.03020.04890.0004-0.1787-0.00210.0513-23.636220.1992-1.6743
41.89390.08840.34791.98250.13962.1140.00160.21710.2318-0.3281-0.07510.0891-0.0039-0.55970.0735-0.11160.0843-0.03320.11610.0217-0.0972-43.19338.5791-17.2676
500.5861.81271.9470.27692.2608-0.0818-0.06070.3453-0.5474-0.2740.0967-0.581-0.0940.35580.01260.1151-0.0824-0.120.02980.0983-31.050523.6252-14.0476
60.62260.97542.49021.01320.17160.9070.0288-0.0477-0.0104-0.0383-0.1907-0.34560.1440.45460.1619-0.1140.08110.0176-0.01720.08440.1096-13.80367.6126-3.6031
74.8537-0.62911.05893.3633-0.52834.7890.05050.15850.09670.2813-0.0998-0.8306-0.13670.3590.0493-0.07110.0203-0.1051-0.1430.00060.026615.3532-4.2992-18.8569
83.0602-0.2293-0.34262.4821-0.00933.69970.05420.36340.4540.1936-0.0744-0.1795-0.5461-0.32460.0202-0.0070.1058-0.0396-0.1010.0586-0.0812.86554.9051-21.6763
90.67850.140.65030.7477-1.87820.1585-0.00980.16420.10340.13370.0117-0.0626-0.0894-0.1999-0.00190.16430.3040.1783-0.04880.2366-0.0483-1.147612.2298-26.4959
101.57410.27871.38411.372-0.37031.77640.34450.2129-0.2594-0.2646-0.0524-0.02860.3669-0.2267-0.2921-0.04860.0556-0.07080.0562-0.0124-0.176-5.4176-13.5971-36.8959
111.6392-0.078-0.9722.5296-0.00420.5298-0.02920.1119-0.0641-0.1290.0658-0.32910.1071-0.0353-0.03650.03250.12990.0060.1487-0.0291-0.17124.6964-12.2211-43.4116
121.573-0.32561.11942.178-0.37591.84780.12060.44620.2687-0.1435-0.1053-0.3348-0.3068-0.0892-0.0154-0.09180.08840.0350.00910.0647-0.16864.9098-0.7621-31.3708
134.6957-0.24551.06032.08470.29962.8676-0.0201-0.09010.2583-0.19330.0015-0.4552-0.24630.25790.0186-0.0548-0.03060.0218-0.09970.0073-0.02389.40894.758423.3365
141.6914-0.03810.21241.03940.05710.62850.1125-0.5295-0.2930.15-0.0657-0.09530.1655-0.111-0.0468-0.0609-0.0216-0.02470.04040.0765-0.0708-0.4937-3.350432.3484
151.3735-0.1138-0.14391.88950.91071.30410.0193-0.13030.07430.05590.03480.079-0.13910.0181-0.0541-0.05050.00520.01210.0943-0.0425-0.1362-17.39213.44937.3546
160.8457-0.6089-0.59510.94640.70861.01810.0002-0.50.11780.03240.1716-0.18-0.07640.2309-0.1718-0.0404-0.0444-0.00280.184-0.1035-0.1015-2.866613.878738.4628
173.44340.198-0.36931.92650.80631.81440.0491-0.5073-0.4060.03610.0385-0.51660.09320.2383-0.0876-0.09480.0076-0.0494-0.02110.05870.091214.124-4.37629.5623
181.5895-0.4059-0.98431.6055-0.03830-0.0436-0.541-0.03970.17060.0888-0.0849-0.01030.182-0.0451-0.0848-0.0012-0.01320.1108-0.0243-0.1918-4.24294.598938.541
193.2471-0.15950.18922.40470.29821.15650.04040.13340.3011-0.2171-0.12870.2163-0.1808-0.35740.0884-0.0580.0633-0.04180.0362-0.0517-0.0193-43.8922-2.13526.1872
201.22410.11410.1380.63770.07480.42680.0087-0.1760.01470.0367-0.08090.0279-0.0224-0.16690.0722-0.050.0117-0.0038-0.014-0.0268-0.0436-31.8269-7.756414.1595
211.5726-0.1698-0.07280.80720.48571.9161-0.00650.0928-0.1617-0.04860.0093-0.10960.12210.1051-0.0028-0.03350.00520.007-0.0533-0.0080.0453-14.061-21.89573.9219
221.1601-0.02740.15890.51810.14330.5970.0108-0.0132-0.1124-0.032-0.06660.06050.028-0.16110.0558-0.0473-0.00940.0001-0.0176-0.0245-0.0104-34.654-16.52985.5632
230.8099-0.1154-0.15491.0634-0.18490.6865-0.0275-0.1125-0.1110.0271-0.01410.1560.0493-0.10490.0416-0.0069-0.01430.0002-0.0194-0.00110.0435-28.4402-22.952813.4123
242.0268-0.2986-1.60370.11090.14593.1172-0.00870.07490.1481-0.04540.0071-0.2723-0.26230.13840.00160.0141-0.0364-0.0066-0.03780.03030.036-11.8818-8.66193.2113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|23 - A|68 }A23 - 68
2X-RAY DIFFRACTION2{ A|69 - A|141 }A69 - 141
3X-RAY DIFFRACTION3{ A|142 - A|253 }A142 - 253
4X-RAY DIFFRACTION4{ A|254 - A|302 }A254 - 302
5X-RAY DIFFRACTION5{ A|303 - A|329 }A303 - 329
6X-RAY DIFFRACTION6{ A|330 - A|344 }A330 - 344
7X-RAY DIFFRACTION7{ B|24 - B|58 }B24 - 58
8X-RAY DIFFRACTION8{ B|59 - B|113 }B59 - 113
9X-RAY DIFFRACTION9{ B|114 - B|121 }B114 - 121
10X-RAY DIFFRACTION10{ B|122 - B|231 }B122 - 231
11X-RAY DIFFRACTION11{ B|232 - B|249 }B232 - 249
12X-RAY DIFFRACTION12{ B|250 - B|343 }B250 - 343
13X-RAY DIFFRACTION13{ C|24 - C|78 }C24 - 78
14X-RAY DIFFRACTION14{ C|79 - C|141 }C79 - 141
15X-RAY DIFFRACTION15{ C|142 - C|197 }C142 - 197
16X-RAY DIFFRACTION16{ C|198 - C|262 }C198 - 262
17X-RAY DIFFRACTION17{ C|263 - C|283 }C263 - 283
18X-RAY DIFFRACTION18{ C|284 - C|344 }C284 - 344
19X-RAY DIFFRACTION19{ D|23 - D|51 }D23 - 51
20X-RAY DIFFRACTION20{ D|52 - D|140 }D52 - 140
21X-RAY DIFFRACTION21{ D|141 - D|198 }D141 - 198
22X-RAY DIFFRACTION22{ D|199 - D|302 }D199 - 302
23X-RAY DIFFRACTION23{ D|303 - D|332 }D303 - 332
24X-RAY DIFFRACTION24{ D|333 - D|343 }D333 - 343

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