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- PDB-4o7m: Crystal structure of a trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4o7m
TitleCrystal structure of a trap periplasmic solute binding protein from shewanella loihica PV-4, target EFI-510273, with bound L-malate
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


organic substance transport / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / C4-dicarboxylate-binding periplasmic protein DctP
Similarity search - Component
Biological speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter, DctP subunit
B: TRAP dicarboxylate transporter, DctP subunit
C: TRAP dicarboxylate transporter, DctP subunit
D: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1889
Polymers149,5564
Non-polymers6325
Water40,1552229
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5232
Polymers37,3891
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6193
Polymers37,3891
Non-polymers2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5232
Polymers37,3891
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5232
Polymers37,3891
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.515, 118.640, 89.901
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TRAP dicarboxylate transporter, DctP subunit


Mass: 37388.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: PV-4 / Gene: Shew_1446 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3QCW5
#2: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2229 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (34.4 mg/ml, 10 mM HEPES, 5 mM DTT, 10 mM L-Malate); Reservoir (0.2 M Sodium Citrate, 20% (w/v) PEG 3350); Cryoprotection (Reservoir with 20% Diethylene Glycol), pH 7.5, VAPOR ...Details: Protein (34.4 mg/ml, 10 mM HEPES, 5 mM DTT, 10 mM L-Malate); Reservoir (0.2 M Sodium Citrate, 20% (w/v) PEG 3350); Cryoprotection (Reservoir with 20% Diethylene Glycol), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX 225 HE / Detector: CCD / Date: Nov 8, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→118.64 Å / Num. all: 268529 / Num. obs: 268529 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 9.42 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.587.40.6011.3288028391730.601100
1.58-1.687.50.4471.7276274370140.447100
1.68-1.797.60.3192.4263078348370.319100
1.79-1.947.60.2233.4246551324060.223100
1.94-2.127.60.1613.6228218298530.161100
2.12-2.377.70.1275.3207592270110.127100
2.37-2.747.70.1025.6183743238080.102100
2.74-3.357.70.0728.2156467202080.072100
3.35-4.747.80.05610.1121371156520.056100
4.74-22.6037.60.0559.96550285670.05599

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→22.603 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.93 / SU ML: 0.11 / σ(F): 0 / σ(I): 0 / Phase error: 13.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1575 13518 5.03 %RANDOM
Rwork0.1381 ---
all0.1391 268483 --
obs0.1391 268483 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.69 Å2 / Biso mean: 13.7201 Å2 / Biso min: 2.87 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9455 0 41 2229 11725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110016
X-RAY DIFFRACTIONf_angle_d1.22113567
X-RAY DIFFRACTIONf_chiral_restr0.0841491
X-RAY DIFFRACTIONf_plane_restr0.0071779
X-RAY DIFFRACTIONf_dihedral_angle_d13.8033763
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.5170.23364470.211485208967
1.517-1.53490.21164220.199584378859
1.5349-1.55360.21114460.190884908936
1.5536-1.57330.20724440.180484998943
1.5733-1.5940.20224580.176284408898
1.594-1.61580.19164460.165984868932
1.6158-1.63890.18054480.162684848932
1.6389-1.66330.17754330.157385188951
1.6633-1.68930.18074480.151284638911
1.6893-1.7170.16294580.143384738931
1.717-1.74660.16064460.137985198965
1.7466-1.77830.16614800.135784108890
1.7783-1.81250.16594340.136785048938
1.8125-1.84950.16934340.13284868920
1.8495-1.88970.14775090.12684528961
1.8897-1.93360.1544540.127384768930
1.9336-1.9820.15944730.127384788951
1.982-2.03550.15034430.125884818924
2.0355-2.09540.14874390.126285248963
2.0954-2.1630.15024570.124484818938
2.163-2.24020.14254530.12185188971
2.2402-2.32980.13484410.118984528893
2.3298-2.43570.14074570.120185418998
2.4357-2.5640.14224550.121985078962
2.564-2.72440.1414410.125485058946
2.7244-2.93430.15824460.136785048950
2.9343-3.22880.15874600.138285489008
3.2288-3.69430.14544340.134785498983
3.6943-4.64780.13024890.122585429031
4.6478-22.60580.17484230.161986789101
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)
10.7657-0.2525-0.08240.42150.09940.2429-0.02010.01480.1705-0.07160.03410.0603-0.0658-0.016-0.01990.0747-0.0056-0.01170.03720.00490.090870.91172.09266.008
20.30910.0519-0.17360.9509-0.18840.2062-0.0099-0.0561-0.01550.0471-0.0099-0.00490.02330.02430.01860.046-0.0115-0.00590.04810.00120.048273.9656.48576.297
30.51560.0510.03520.6417-0.07430.6436-0.020.0119-0.0322-0.0847-0.0232-0.06070.11920.11910.03440.07560.01170.01830.0640.0080.063985.5449.74359.288
40.3337-0.358-0.20271.83330.81780.7276-0.0157-0.08840.05360.1784-0.0344-0.03080.0884-0.03450.0070.0478-0.0087-0.00320.062-0.01840.072571.42666.02877.055
50.846-0.6165-0.87831.32281.34451.98560.00280.03490.0512-0.0370.00730.04980.0084-0.04830.02750.0506-0.0076-0.02080.04680.00030.076165.01861.01463.154
60.277-0.033-0.13570.0643-0.06910.7059-0.0386-0.0342-0.2252-0.1497-0.00830.06760.29630.06360.01860.1361-0.00120.00720.05730.02980.101278.47239.82967.994
70.53380.04430.00930.4050.10830.54360.00540.0017-0.1196-0.0035-0.0070.04480.0745-0.0642-0.00550.05450.0080.00430.05-0.00260.07734.93634.66165.033
80.32440.3034-0.05241.45410.42421.68810.01950.06040.072-0.08-0.0418-0.0975-0.07280.01030.02740.05130.0203-0.00150.05660.0130.060238.456.16658.666
90.39920.21170.30120.42370.29350.5132-0.00630.01280.086-0.0765-0.00980.0057-0.069-0.0477-0.00170.07310.0276-0.00110.07910.00560.086433.94555.24662.208
100.31710.04280.05940.34420.02610.1742-0.01060.01360.024-0.0224-0.0139-0.0226-0.0165-0.02170.02590.04070.01480.00090.04870.00280.064243.13252.45770.27
110.64820.44810.63811.30561.29961.99870.0229-0.0286-0.03420.0264-0.02270.07910.0453-0.15930.0060.03870.00370.00670.0913-0.00130.082325.98244.22569.783
120.32410.04370.16170.25990.07850.8975-0.03690.01030.1711-0.0210.00320.0059-0.1545-0.00660.00720.0950.03670.00030.09170.02220.159437.02166.87865.733
130.45310.13560.03080.45040.0410.83540.029-0.15180.06040.21-0.04470.0494-0.106-0.00870.02370.08510.00270.01090.07780.00360.068450.74440.5296.239
140.570.0464-0.03630.3239-0.23390.2780.0162-0.02070.03280.0162-0.0187-0.0014-0.0992-0.00960.00380.04680.00010.00150.04050.0130.04756.04241.79488.104
151.08830.18530.18781.29930.27480.34090.02510.09350.0053-0.0965-0.0212-0.10580.0660.00370.01430.04690.01480.00440.07020.03240.056161.58820.70686.206
160.40690.06260.14810.48540.03430.56550.01440.0101-0.0259-0.0057-0.0281-0.07690.0704-0.0028-0.00120.06140.0090.00280.06540.0330.07557.83420.76290.757
171.65730.05870.23052.00640.34071.1881-0.00870.05730.0115-0.0809-0.0489-0.05570.05260.00270.04430.09140.00110.0090.07170.02680.04752.8516.72475.827
180.7983-0.4753-0.08990.93080.0250.80790.05210.13030.0198-0.1613-0.01460.08460.0105-0.1088-0.01340.0616-0.0079-0.01270.07730.03040.05345.09222.99675.357
190.42330.23370.09420.52510.00920.46520.0062-0.0420.0191-0.0002-0.02390.03950.0063-0.06320.00590.02780.0013-0.00070.05310.02240.047350.41627.19288.867
201.54361.09360.57751.47490.41970.5433-0.0177-0.1205-0.04430.1388-0.0140.0275-0.0539-0.11770.00750.0821-0.02570.02260.11130.00460.04149.5730.18399.865
210.77680.08110.22080.2110.07980.35430.01190.0407-0.10840.0019-0.00480.010.2388-0.0237-0.01970.10040.00430.00820.0820.03990.092855.5779.65986.427
220.39090.0676-0.04470.3854-0.1930.9114-0.1126-0.1221-0.09790.21980.0841-0.08360.16470.06740.02660.14940.04550.00450.1028-0.00170.070165.1958.2848.745
230.3153-0.1174-0.06341.9225-0.02670.1679-0.0090.0262-0.04970.0075-0.02370.15270.0289-0.01910.03140.06060.00110.01090.0687-0.02560.056153.94420.06440.496
240.68860.1153-0.21411.79910.35770.7964-0.08780.0239-0.02320.12220.02730.18780.0092-0.01820.04980.10360.01870.02540.0806-0.02230.081650.77823.10749.592
250.5371-0.11380.14940.60320.05290.5594-0.03530.04080.0155-0.03780.0226-0.0608-0.02770.06650.01310.08-0.00590.00390.0954-0.0150.053767.57529.73431.905
260.39710.2091-0.12740.9086-0.20260.3863-0.0698-0.0335-0.00360.04280.0650.130.0664-0.00430.01550.08740.0090.01150.0774-0.01980.054258.6119.71744.544
270.95760.7773-0.58221.341-0.69590.7313-0.0225-0.16850.00030.29940.0418-0.07970.02440.0556-0.00980.16730.03780.0020.1293-0.01410.034466.25320.18453.833
280.61970.1425-0.18790.31010.0190.4089-0.04870.09670.1025-0.01270.02260.0493-0.1532-0.0391-0.00140.09390.009-0.01770.0778-0.03160.062857.78639.11338.928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 33:82 )A33 - 82
2X-RAY DIFFRACTION2( CHAIN A AND RESID 83:152 )A83 - 152
3X-RAY DIFFRACTION3( CHAIN A AND RESID 153:238 )A153 - 238
4X-RAY DIFFRACTION4( CHAIN A AND RESID 239:256 )A239 - 256
5X-RAY DIFFRACTION5( CHAIN A AND RESID 257:292 )A257 - 292
6X-RAY DIFFRACTION6( CHAIN A AND RESID 293:336 )A293 - 336
7X-RAY DIFFRACTION7( CHAIN B AND RESID 32:98 )B32 - 98
8X-RAY DIFFRACTION8( CHAIN B AND RESID 99:120 )B99 - 120
9X-RAY DIFFRACTION9( CHAIN B AND RESID 121:170 )B121 - 170
10X-RAY DIFFRACTION10( CHAIN B AND RESID 171:256 )B171 - 256
11X-RAY DIFFRACTION11( CHAIN B AND RESID 257:292 )B257 - 292
12X-RAY DIFFRACTION12( CHAIN B AND RESID 293:336 )B293 - 336
13X-RAY DIFFRACTION13( CHAIN C AND RESID 32:62 )C32 - 62
14X-RAY DIFFRACTION14( CHAIN C AND RESID 63:98 )C63 - 98
15X-RAY DIFFRACTION15( CHAIN C AND RESID 99:120 )C99 - 120
16X-RAY DIFFRACTION16( CHAIN C AND RESID 121:170 )C121 - 170
17X-RAY DIFFRACTION17( CHAIN C AND RESID 171:190 )C171 - 190
18X-RAY DIFFRACTION18( CHAIN C AND RESID 191:217 )C191 - 217
19X-RAY DIFFRACTION19( CHAIN C AND RESID 218:256 )C218 - 256
20X-RAY DIFFRACTION20( CHAIN C AND RESID 257:292 )C257 - 292
21X-RAY DIFFRACTION21( CHAIN C AND RESID 293:312 )C293 - 312
22X-RAY DIFFRACTION22( CHAIN D AND RESID 33:82 )D33 - 82
23X-RAY DIFFRACTION23( CHAIN D AND RESID 83:120 )D83 - 120
24X-RAY DIFFRACTION24( CHAIN D AND RESID 121:152 )D121 - 152
25X-RAY DIFFRACTION25( CHAIN D AND RESID 153:229 )D153 - 229
26X-RAY DIFFRACTION26( CHAIN D AND RESID 230:256 )D230 - 256
27X-RAY DIFFRACTION27( CHAIN D AND RESID 257:292 )D257 - 292
28X-RAY DIFFRACTION28( CHAIN D AND RESID 293:335 )D293 - 335

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