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- PDB-7xjn: Structure of VcPotD1 in complex with norspermidine -

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Basic information

Entry
Database: PDB / ID: 7xjn
TitleStructure of VcPotD1 in complex with norspermidine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / PotD family / polyamine binding protein / norspermidine / Vibrio cholerae
Function / homologypolyamine binding / polyamine transport / Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / N-(3-aminopropyl)propane-1,3-diamine / 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: 1.79 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 norspermidine
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:
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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)149,34411
Polymers148,1484
Non-polymers1,1967
Water13,025723
1
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3623
Polymers37,0371
Non-polymers3252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1682
Polymers37,0371
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4513
Polymers37,0371
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3623
Polymers37,0371
Non-polymers3252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.640, 87.410, 174.430
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-NSD / N-(3-aminopropyl)propane-1,3-diamine / Norspermidine


Mass: 131.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H17N3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystal of VcPotD1 in complex with norspermidine was obtained 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 norspermidine for 2 ...Details: The crystal of VcPotD1 in complex with norspermidine was obtained 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 norspermidine 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: 1.787→174.428 Å / Num. obs: 124265 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rpim(I) all: 0.022 / Rrim(I) all: 0.081 / Rsym value: 0.078 / Net I/σ(I): 20.1
Reflection shellResolution: 1.787→1.793 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1214 / CC1/2: 0.845 / Rpim(I) all: 0.294 / Rrim(I) all: 1.097 / Rsym value: 1.057 / % possible all: 99.8

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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: 1.79→87.21 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.125 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.21 6257 5.07 %RANDOM
Rwork0.183 ---
obs0.185 123463 99.8 %-
Displacement parametersBiso max: 148.01 Å2 / Biso mean: 37.59 Å2 / Biso min: 13.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.8687 Å20 Å20 Å2
2---3.3013 Å20 Å2
3---4.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.79→87.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10275 0 81 723 11079
Biso mean--43.12 38.19 -
Num. residues----1278
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3650SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes280HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1476HARMONIC5
X-RAY DIFFRACTIONt_it10654HARMONIC20
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_contact13099SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10654HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14433HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion17.93
LS refinement shellResolution: 1.79→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 495 5.49 %
Rwork0.211 8514 -
all0.213 9009 -
obs--99.9 %
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)
11.5159-0.18040.55352.1655-0.11251.71970.1224-0.0074-0.0896-0.0357-0.11310.05160.2684-0.2801-0.0093-0.10010.0068-0.0062-0.02330.0096-0.1203-38.2833-1.0787-10.5681
21.36920.09390.27451.6046-0.48591.12410.02880.37090.2905-0.1703-0.1398-0.0822-0.1155-0.12110.111-0.07940.09540.03190.04780.1146-0.0419-32.145112.1989-17.7476
30.88240.0172-0.32181.215-0.21382.49230.07490.04520.27820.1069-0.1463-0.1896-0.44160.06770.0713-0.10850.0317-0.018-0.15450.0630.0067-24.182118.2734-3.1089
41.64070.45710.72082.1461-0.22521.9345-0.09390.19440.2771-0.35230.00990.2481-0.0472-0.3470.084-0.14860.0739-0.0410.0530.0504-0.0815-44.982310.5256-17.0101
501.37881.16561.1826-0.05282.078-0.04680.00980.3395-0.4199-0.21210.0099-0.45850.06790.2589-0.03210.0769-0.0564-0.110.09920.0518-30.364823.2686-14.2431
60.57661.51011.45920.8749-0.66424.23870.0709-0.0492-0.0033-0.1115-0.3239-0.62120.37470.83520.253-0.11530.08470.0484-0.00990.13050.1064-13.82957.6307-3.8433
72.5946-0.64240.81833.7382-0.23473.84340.16160.26590.00260.3086-0.0364-0.47910.17560.0392-0.1252-0.10870.0223-0.0457-0.1537-0.0003-0.11979.4405-3.7048-18.9757
85.8726-0.7148-0.25973.1843-1.63574.97420.02920.78010.98690.1619-0.0673-0.2877-1.0256-0.44940.0380.01480.14650.0115-0.16530.1363-0.06823.439410.9775-24.1013
93.1396-0.52982.10272.127-1.46722.54530.68710.2925-0.6109-0.6875-0.03220.31620.8087-0.2095-0.65480.01710.0486-0.23360.015-0.0406-0.2173-6.4505-13.9535-37.3229
102.4293-0.89871.35151.9641-0.8143.69810.43680.7923-0.2117-0.5275-0.2092-0.07360.58380.2662-0.2277-0.00280.1673-0.02030.1109-0.0379-0.2294.2777-8.7612-36.5229
112.9717-1.71473.13614.2432-1.81042.5114-0.07970.54560.71180.2906-0.1141-0.9275-0.72320.39560.1938-0.1556-0.0564-0.0393-0.20340.1050.060716.50045.3978-21.9455
124.6142-0.55472.01432.4853-0.71231.84940.23580.54310.1338-0.4818-0.1477-0.07870.03930.132-0.0881-0.10860.1720.03930.10680.0694-0.31731.4905-2.9105-35.7774
133.3233-0.1860.39921.84120.73692.84690.0848-0.06080.1484-0.13250.0248-0.466-0.27360.4327-0.1096-0.0861-0.05240.0102-0.0695-0.0018-0.024913.65734.869325.761
141.61960.19060.41341.15250.65261.44450.1315-0.3953-0.23030.1086-0.1064-0.0760.1346-0.1162-0.0252-0.091-0.0402-0.033-0.05990.0561-0.1095-0.3662-1.661529.745
151.05280.31550.30561.96931.35491.67090.0525-0.19470.09850.08940.01080.1176-0.1824-0.0592-0.0633-0.0494-0.00150.01720.1003-0.0533-0.1233-17.606413.621837.2323
160.8456-0.4336-0.26390.28840.28460.8491-0.0295-0.51760.09770.05430.1223-0.1337-0.08620.1334-0.0928-0.0288-0.0481-0.01350.155-0.0938-0.1011-2.581213.723738.5213
172.8602-0.2783-0.17012.13821.11972.95890.073-0.8053-0.20510.30470.0541-0.2390.19260.1899-0.127-0.1246-0.0206-0.07820.03040.0712-0.1199.824-0.439239.0987
180.9935-0.1942-0.01651.2525-0.81532.59360.0575-0.1552-0.02820.02570.0670.1572-0.14630.2314-0.1245-0.0394-0.0335-0.00350.0754-0.0227-0.0868-13.92876.444632.1444
193.0176-0.6076-0.26163.00660.16031.31870.15770.14430.1397-0.2932-0.19190.2709-0.1891-0.30490.0342-0.05710.0635-0.0434-0.0253-0.0407-0.0364-43.8251-2.33796.1472
201.44320.03850.00360.76010.13830.47670.0302-0.15610.01080.0457-0.10410.0429-0.0252-0.10650.0739-0.0955-0.0004-0.0068-0.0851-0.0154-0.0929-31.7184-7.731314.2156
211.5063-0.05080.07290.87110.64371.55630.03850.123-0.1696-0.0552-0.0368-0.10920.06330.0391-0.0017-0.02350.00750.0032-0.0461-0.01180.0497-16.4932-20.82831.5344
221.1747-0.09920.0270.75720.27940.60090.0223-0.0386-0.12430.0101-0.08310.08270.0144-0.15080.0608-0.064-0.01470.0028-0.0408-0.0118-0.0264-37.105-16.40838.3386
230.4044-0.7835-0.12980.811-0.22050.57050.0309-0.1276-0.21020.0918-0.03860.09830.073-0.09210.00770.0048-0.01740.0003-0.02850.00520.0372-28.3707-23.044213.4524
242.3844-2.0867-0.53470.1088-0.51338.07830.10870.19430.2452-0.0907-0.0485-0.4042-0.39110.2817-0.06020.0029-0.02990.0019-0.06030.03270.0377-11.963-8.73843.3058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|23 - A|78 }A23 - 78
2X-RAY DIFFRACTION2{ A|79 - A|146 }A79 - 146
3X-RAY DIFFRACTION3{ A|147 - A|262 }A147 - 262
4X-RAY DIFFRACTION4{ A|263 - A|303 }A263 - 303
5X-RAY DIFFRACTION5{ A|304 - A|329 }A304 - 329
6X-RAY DIFFRACTION6{ A|330 - A|344 }A330 - 344
7X-RAY DIFFRACTION7{ B|24 - B|83 }B24 - 83
8X-RAY DIFFRACTION8{ B|84 - B|124 }B84 - 124
9X-RAY DIFFRACTION9{ B|125 - B|218 }B125 - 218
10X-RAY DIFFRACTION10{ B|219 - B|262 }B219 - 262
11X-RAY DIFFRACTION11{ B|263 - B|283 }B263 - 283
12X-RAY DIFFRACTION12{ B|284 - B|343 }B284 - 343
13X-RAY DIFFRACTION13{ C|23 - C|58 }C23 - 58
14X-RAY DIFFRACTION14{ C|59 - C|141 }C59 - 141
15X-RAY DIFFRACTION15{ C|142 - C|198 }C142 - 198
16X-RAY DIFFRACTION16{ C|199 - C|262 }C199 - 262
17X-RAY DIFFRACTION17{ C|263 - C|312 }C263 - 312
18X-RAY DIFFRACTION18{ C|313 - C|344 }C313 - 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|218 }D141 - 218
22X-RAY DIFFRACTION22{ D|219 - D|302 }D219 - 302
23X-RAY DIFFRACTION23{ D|303 - D|332 }D303 - 332
24X-RAY DIFFRACTION24{ D|333 - D|343 }D333 - 343

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