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- PDB-5t1p: Crystal structure of the putative periplasmic solute-binding prot... -

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Basic information

Entry
Database: PDB / ID: 5t1p
TitleCrystal structure of the putative periplasmic solute-binding protein from Campylobacter jejuni
ComponentsABC transporter, periplasmic substrate-binding protein
KeywordsHYDROLASE / cell envelope / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyL-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesCampylobacter jejuni BJ-CJGB96299 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFilippova, E.V. / Wawrzsak, Z. / Sandoval, J. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of the putative periplasmic solute-binding protein from Campylobacter jejuni
Authors: Filippova, E.V. / Wawrzsak, Z. / Sandoval, J. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 30, 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: ABC transporter, periplasmic substrate-binding protein
B: ABC transporter, periplasmic substrate-binding protein
C: ABC transporter, periplasmic substrate-binding protein
D: ABC transporter, periplasmic substrate-binding protein
E: ABC transporter, periplasmic substrate-binding protein
F: ABC transporter, periplasmic substrate-binding protein
G: ABC transporter, periplasmic substrate-binding protein
H: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,60720
Polymers309,6598
Non-polymers1,94812
Water29,1661619
1
A: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0293
Polymers38,7071
Non-polymers3212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9222
Polymers38,7071
Non-polymers2151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9222
Polymers38,7071
Non-polymers2151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9222
Polymers38,7071
Non-polymers2151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0233
Polymers38,7071
Non-polymers3152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9363
Polymers38,7071
Non-polymers2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9172
Polymers38,7071
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9363
Polymers38,7071
Non-polymers2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.190, 89.276, 100.394
Angle α, β, γ (deg.)68.88, 82.52, 70.66
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
ABC transporter, periplasmic substrate-binding protein


Mass: 38707.344 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni BJ-CJGB96299 (Campylobacter)
Gene: K680_1691 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A0W8LFT3

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Non-polymers , 5 types, 1631 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GPE / L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE


Mass: 215.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H14NO6P
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1619 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 25% P3350, 0.1M B-Tris pH 6.5, MgSulphate 1mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2016 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 167225 / % possible obs: 98.1 % / Redundancy: 11.8 % / CC1/2: 0.9 / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.7 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.061 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22393 8289 5.1 %RANDOM
Rwork0.17571 ---
obs0.17815 155567 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.194 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20.2 Å2-0.19 Å2
2--0.36 Å2-0.13 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20409 0 115 1619 22143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221157
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220461
X-RAY DIFFRACTIONr_angle_refined_deg1.731.95628688
X-RAY DIFFRACTIONr_angle_other_deg0.924347189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.93352651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26725.825939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.553153643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1831568
X-RAY DIFFRACTIONr_chiral_restr0.1150.23161
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0224027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8451.28610561
X-RAY DIFFRACTIONr_mcbond_other0.8441.28510558
X-RAY DIFFRACTIONr_mcangle_it1.4051.9213225
X-RAY DIFFRACTIONr_mcangle_other1.4051.9213226
X-RAY DIFFRACTIONr_scbond_it1.011.4210596
X-RAY DIFFRACTIONr_scbond_other1.0081.4210596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6462.06715464
X-RAY DIFFRACTIONr_long_range_B_refined5.0716.09525090
X-RAY DIFFRACTIONr_long_range_B_other5.0716.09625091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 461 -
Rwork0.22 9001 -
obs--74.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.60280.0402-0.76791.98350.20721.2108-0.18540.0168-0.36190.05320.0744-0.08910.2550.15920.1110.1690.0290.01580.03510.0250.1766.3341.044933.3618
21.9203-0.0122-0.2790.9150.31461.1816-0.09670.00090.04740.07270.02070.04440.0137-0.09580.0760.1146-0.0156-0.00720.01830.01390.094848.870913.825637.6542
32.8999-0.2965-0.30910.80030.29781.4342-0.12430.1807-0.37560.05020.0262-0.02750.2636-0.05880.09810.1845-0.04470.03430.0283-0.00570.179453.34051.641931.5358
42.58231.32150.01973.01340.75192.4658-0.15360.0366-0.0151-0.09880.0555-0.0462-0.086-0.11470.09810.05630.0108-0.020.01910.01790.10245.140517.274335.0754
53.00420.8644-0.08822.10590.63472.2742-0.0441-0.1017-0.31490.00360.1272-0.25180.2180.6791-0.08310.14210.0780.0150.22860.030.13175.108728.58-12.6548
61.6319-0.0017-0.00310.95050.83623.1556-0.0318-0.05960.04450.0186-0.0580.03290.006-0.10570.08980.1142-0.01130.00610.02410.03630.114558.148435.001-8.7502
73.5739-3.1352-5.30033.3263.90158.8447-0.20930.0177-0.13340.07520.02540.1180.4169-0.06130.18390.1606-0.0892-0.02760.05690.04690.206550.835916.7479-13.073
81.61861.0561.42123.10331.81294.2197-0.12970.05270.2529-0.1331-0.0556-0.0892-0.6427-0.18960.18530.1790.0432-0.02120.02850.04390.192254.609845.289-9.9901
93.27710.8663-0.63222.70850.17311.2210.1195-0.30510.05410.1896-0.28820.27190.2134-0.30990.16860.1014-0.05640.01070.2179-0.09260.083864.241613.429163.6368
101.45180.054-0.41861.2881.15963.23810.01650.06770.125-0.0672-0.0384-0.10840.0368-0.10030.02190.05710.0313-0.0140.06280.00650.061383.142517.917551.7931
113.13430.0743-0.46841.40020.82832.44470.0796-0.3924-0.07360.2139-0.1777-0.00810.3561-0.21390.09810.1112-0.0298-0.02510.1103-0.01240.036177.302412.635965.2787
122.3326-0.84341.77182.4745-0.28834.2284-0.0808-0.13770.04950.08960.15260.0461-0.18040.0249-0.07180.01040.00170.00350.02580.01640.061984.020122.529453.201
133.26890.5142-0.50631.323-0.5561.486-0.04350.1995-0.2126-0.00930.07520.04380.0111-0.2115-0.03170.0755-0.03110.0010.04840.00750.084671.99539.861718.9062
143.0110.0477-0.41370.6776-0.02231.2882-0.00630.311-0.1316-0.0924-0.0059-0.03550.04830.02920.01220.1132-0.03710.00760.05960.00840.088688.650842.68211.4276
157.2289-4.4407-6.576711.0904-1.3479.4543-0.4565-0.4252-0.04570.10390.3004-0.15130.52540.36990.15610.11680.0337-0.10040.2808-0.05580.219596.36631.275827.3195
164.2661-1.38031.81112.822-0.48893.88860.01980.52870.2546-0.0655-0.10730.0109-0.32090.0810.08750.093-0.01580.02190.11890.07380.119492.261651.17376.7387
172.0946-0.1823-1.15931.15190.25374.6771-0.0255-0.3582-0.13850.0436-0.0467-0.02720.04520.07760.07220.0870.00580.00910.08790.05980.0718100.161757.079849.8833
182.2121-0.7463-0.10261.67320.11991.96460.14420.147-0.0173-0.0589-0.0066-0.0382-0.02310.1965-0.13760.1058-0.00770.00860.0361-0.00190.1377118.856745.4423.7919
191.6316-0.4283-1.1160.89511.07882.63990.088-0.04560.0219-0.1216-0.0288-0.0397-0.2298-0.1005-0.05920.15160.00120.02420.02870.04880.1364105.873256.996632.8941
209.2213-0.5064-5.2341.2642-0.86835.06630.0901-0.288-0.18380.2423-0.0237-0.0187-0.21020.2397-0.06640.1115-0.0026-0.04710.01490.00770.101123.389538.861336.4619
211.1460.11050.76691.73281.16184.41090.05870.1253-0.1327-0.0005-0.09110.12360.1291-0.1140.03250.0535-0.03360.01420.0535-0.03620.099559.913956.029545.824
222.87670.5561-0.17061.76130.26033.03640.1149-0.15850.06270.1204-0.03310.1713-0.0098-0.4833-0.08170.0147-0.00480.02380.2255-0.0030.051841.25262.687973.5325
231.173-0.1415-0.53770.60480.05672.57580.06420.06940.03580.00070.02880.0518-0.33-0.244-0.0930.0773-0.00230.02540.05890.00370.076953.738766.63659.1254
2411.4279-3.2222-3.54962.16221.77742.6631-0.0080.0462-0.5652-0.1782-0.05880.10010.194-0.37050.06680.1161-0.0935-0.00370.11860.02670.106437.99549.181168.1761
252.3916-0.67360.7381.37750.49183.50410.0268-0.310.20450.1-0.1595-0.05620.1146-0.7210.13260.015-0.03220.01160.172-0.03680.034578.8623-3.16542.2703
263.2806-1.2691-0.97191.63121.61863.28220.28790.49230.1025-0.1829-0.1662-0.1476-0.0544-0.0964-0.12170.12580.04910.02980.09480.05820.113296.3786-13.1694-23.6133
273.156-0.8378-0.9971.04521.4212.79630.34750.20090.4807-0.3015-0.2816-0.1155-0.3775-0.4419-0.0660.17450.07060.05250.09540.06150.181685.422-1.4141-13.7974
285.4422-1.9106-0.4222.8180.72342.5697-0.0050.1591-0.09740.2667-0.09570.00970.0753-0.20240.10070.0771-0.0066-0.0070.0189-0.00980.006692.9476-15.4427-16.1847
293.5296-0.55240.23633.04440.19162.76150.30721.3256-0.4536-0.1371-0.31690.33250.10370.04460.00960.07730.0037-0.00420.8427-0.32650.149836.4042-3.5115-5.7656
302.7766-0.0150.0820.74840.14231.57230.01710.1844-0.04390.02960.09770.0514-0.041-0.0398-0.11490.0846-0.07720.01910.1398-0.05630.1224.70592.289818.4596
313.5562-0.7581-0.92550.72580.12352.7492-0.01820.8155-0.1715-0.0780.0010.0924-0.09630.05240.01730.0907-0.09270.01070.3517-0.12130.182131.12022.57018.6292
323.31290.05510.03180.14670.04371.63180.01750.5184-0.1950.01360.0711-0.04980.00140.2074-0.08860.0569-0.05430.04320.1982-0.11260.072932.21660.731712.7742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 80
2X-RAY DIFFRACTION2A81 - 236
3X-RAY DIFFRACTION3A237 - 304
4X-RAY DIFFRACTION4A305 - 348
5X-RAY DIFFRACTION5B22 - 97
6X-RAY DIFFRACTION6B98 - 301
7X-RAY DIFFRACTION7B302 - 309
8X-RAY DIFFRACTION8B310 - 347
9X-RAY DIFFRACTION9C23 - 104
10X-RAY DIFFRACTION10C105 - 234
11X-RAY DIFFRACTION11C235 - 302
12X-RAY DIFFRACTION12C303 - 348
13X-RAY DIFFRACTION13D20 - 99
14X-RAY DIFFRACTION14D100 - 301
15X-RAY DIFFRACTION15D302 - 308
16X-RAY DIFFRACTION16D309 - 347
17X-RAY DIFFRACTION17E22 - 132
18X-RAY DIFFRACTION18E133 - 205
19X-RAY DIFFRACTION19E206 - 323
20X-RAY DIFFRACTION20E324 - 347
21X-RAY DIFFRACTION21F21 - 131
22X-RAY DIFFRACTION22F132 - 205
23X-RAY DIFFRACTION23F206 - 322
24X-RAY DIFFRACTION24F323 - 347
25X-RAY DIFFRACTION25G22 - 127
26X-RAY DIFFRACTION26G128 - 205
27X-RAY DIFFRACTION27G206 - 305
28X-RAY DIFFRACTION28G306 - 347
29X-RAY DIFFRACTION29H21 - 102
30X-RAY DIFFRACTION30H103 - 236
31X-RAY DIFFRACTION31H237 - 268
32X-RAY DIFFRACTION32H269 - 347

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