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- PDB-5mkb: Maltodextrin binding protein MalE1 from L. casei BL23 without ligand -

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Basic information

Entry
Database: PDB / ID: 5mkb
TitleMaltodextrin binding protein MalE1 from L. casei BL23 without ligand
ComponentsMalE1
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding protein / lactobacillus casei
Function / homologyBacterial extracellular solute-binding protein / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / MalE1
Function and homology information
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsHomburg, C. / Bommer, M. / Wuttge, S. / Hobe, C. / Beck, S. / Dobbek, H. / Deutscher, J. / Licht, A. / Schneider, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1078 Germany
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Inducer exclusion in Firmicutes: insights into the regulation of a carbohydrate ATP binding cassette transporter from Lactobacillus casei BL23 by the signal transducing protein P-Ser46-HPr.
Authors: Homburg, C. / Bommer, M. / Wuttge, S. / Hobe, C. / Beck, S. / Dobbek, H. / Deutscher, J. / Licht, A. / Schneider, E.
History
DepositionDec 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MalE1
B: MalE1
C: MalE1
D: MalE1
E: MalE1
F: MalE1
G: MalE1
H: MalE1


Theoretical massNumber of molelcules
Total (without water)324,0388
Polymers324,0388
Non-polymers00
Water41,7052315
1
A: MalE1


Theoretical massNumber of molelcules
Total (without water)40,5051
Polymers40,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MalE1


Theoretical massNumber of molelcules
Total (without water)40,5051
Polymers40,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MalE1


Theoretical massNumber of molelcules
Total (without water)40,5051
Polymers40,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MalE1


Theoretical massNumber of molelcules
Total (without water)40,5051
Polymers40,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: MalE1


Theoretical massNumber of molelcules
Total (without water)40,5051
Polymers40,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: MalE1


Theoretical massNumber of molelcules
Total (without water)40,5051
Polymers40,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: MalE1


Theoretical massNumber of molelcules
Total (without water)40,5051
Polymers40,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: MalE1


Theoretical massNumber of molelcules
Total (without water)40,5051
Polymers40,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-14 kcal/mol
Surface area121120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.036, 124.945, 143.739
Angle α, β, γ (deg.)74.51, 89.61, 89.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
MalE1


Mass: 40504.734 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: malE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0L7B0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2315 / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 mM Na-Hepes, pH 7.0, 20-25% Jeffamine ED2003, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.698→46.171 Å / Num. obs: 294468 / % possible obs: 96.91 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 15.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0678 / Net I/σ(I): 13.21
Reflection shellResolution: 1.698→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.663 / % possible all: 93.21

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSVERSION November 3, 2014data reduction
XDSVERSION November 3, 2014data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M28
Resolution: 1.698→46.171 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.22
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 15201 5.16 %random selection
Rwork0.1782 ---
obs0.1814 294468 96.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 1.698→46.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22424 0 0 2315 24739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322896
X-RAY DIFFRACTIONf_angle_d0.79531080
X-RAY DIFFRACTIONf_dihedral_angle_d13.0068232
X-RAY DIFFRACTIONf_chiral_restr0.0313504
X-RAY DIFFRACTIONf_plane_restr0.0044000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6983-1.72760.30646910.270413125X-RAY DIFFRACTION87
1.7276-1.7590.30547340.265513949X-RAY DIFFRACTION92
1.759-1.79290.31027340.253713898X-RAY DIFFRACTION91
1.7929-1.82950.29887410.243413877X-RAY DIFFRACTION92
1.8295-1.86920.27867280.229314035X-RAY DIFFRACTION92
1.8692-1.91270.26947280.2313870X-RAY DIFFRACTION92
1.9127-1.96060.26177370.222214045X-RAY DIFFRACTION92
1.9606-2.01360.25797340.204713913X-RAY DIFFRACTION92
2.0136-2.07280.23987370.200813991X-RAY DIFFRACTION92
2.0728-2.13970.22457300.194714053X-RAY DIFFRACTION92
2.1397-2.21620.22427370.192813981X-RAY DIFFRACTION93
2.2162-2.30490.23737310.190214123X-RAY DIFFRACTION92
2.3049-2.40980.23327480.184514115X-RAY DIFFRACTION93
2.4098-2.53690.21927310.177114062X-RAY DIFFRACTION93
2.5369-2.69580.20177380.172514018X-RAY DIFFRACTION93
2.6958-2.90390.22267460.178214225X-RAY DIFFRACTION93
2.9039-3.19610.20357430.169914163X-RAY DIFFRACTION93
3.1961-3.65840.20427530.156614041X-RAY DIFFRACTION93
3.6584-4.60850.17217370.134514025X-RAY DIFFRACTION92
4.6085-46.18810.17827510.15214243X-RAY DIFFRACTION94
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)
11.9404-0.14820.10880.7051-0.47360.6062-0.04830.11260.0081-0.0783-0.04420.0061-0.0205-0.08940.01820.1650.0115-0.01750.26370.10440.2609-34.3425179.5107-56.5098
20.38240.03760.08630.47070.11980.2792-0.05190.12080.19350.05430.0039-0.0684-0.0147-0.04390.02360.126-0.03-0.04430.14520.04860.1509-28.6605168.9092-48.596
30.5199-0.0350.12360.35290.05680.5289-0.10220.0985-0.0275-0.1130.01960.02310.0819-0.05450.01890.1436-0.07130.01730.1373-0.00160.0791-35.847142.9293-55.0782
40.28610.0709-0.07520.5314-0.08770.3177-0.10580.10820.0651-0.05660.0654-0.0290.0151-0.07660.01940.0829-0.046-0.00620.13690.02590.0881-31.0214157.8027-49.3734
51.38040.2275-0.00541.08060.0970.77440.0272-0.1735-0.110.03690.0023-0.01470.0950.08590.00340.1634-0.01160.04870.20840.11840.2725-52.894274.5388-45.8662
60.4692-0.1564-0.27630.56020.15340.42950.0259-0.1114-0.04760.0085-0.00480.0266-0.00420.1132-0.01270.0714-0.01080.03770.11930.00570.1613-47.335188.5592-54.8678
70.6364-0.0699-0.21240.2780.0590.3878-0.006-0.0823-0.03820.0984-0.01310.1961-0.0476-0.004-0.01770.1272-0.00170.07110.1074-0.01210.1748-55.0904112.7165-48.6347
80.37840.1777-0.05620.68120.00770.45050.0508-0.1158-0.05090.1009-0.00960.08840.06180.0010.03820.09-0.00420.03360.11430.04530.2052-54.776383.3659-52.6838
90.25310.06490.01170.40080.00080.33670.0403-0.0579-0.05840.0723-0.03750.0927-0.04720.051-0.0190.085-0.01720.04740.1004-0.00990.1625-46.7377108.0018-54.2267
101.62-0.067-0.2230.8814-0.28390.6027-0.0498-0.0544-0.0874-0.00930.0503-0.03050.1046-0.0528-0.00310.2390.02360.10740.33930.13710.3228-33.9927113.8392-12.4707
110.5197-0.1549-0.25630.69630.09920.4642-0.105-0.0646-0.1761-0.0463-0.0263-0.15020.040.00030.02610.17010.05990.10090.16370.05330.1736-26.7076126.4373-21.8955
120.3982-0.0593-0.06820.29870.14760.2984-0.1951-0.16910.04050.14970.06480.0493-0.1202-0.0261-0.0540.24520.1438-0.02690.1929-0.03670.1053-36.0181151.8453-12.9898
130.5175-0.047-0.03470.4181-0.03060.4186-0.221-0.2086-0.12080.13720.08310.047-0.0625-0.0541-0.07080.13190.10060.04160.17670.01730.1291-30.8751137.2175-19.0298
141.6726-0.094-0.22730.9133-0.17770.8233-0.0015-0.0997-0.00150.01350.0344-0.0432-0.02470.0204-0.01060.1268-0.02050.03580.20910.04620.1583-31.214160.6204-77.4557
150.1995-0.06940.060.3446-0.0080.09820.0453-0.061-0.0779-0.0288-0.0366-0.04230.03060.00090.01610.1085-0.01450.06060.12410.00920.1688-25.4307170.6844-86.1874
160.5777-0.0305-0.16990.29350.06930.2269-0.0628-0.1572-0.01180.02440.00840.01950.03060.01010.03740.09080.02580.0210.1439-0.00440.1035-32.4509196.574-81.288
170.20.06110.10210.47620.00050.2-0.0694-0.0608-0.0245-0.01950.06160.07010.02520.00590.00860.06560.01890.03990.12410.00230.1177-28.9807183.6263-87.0913
181.0279-0.82860.23010.7775-0.11020.1545-0.05260.21370.2681-0.0629-0.01920.0721-0.09830.0994-0.04860.1933-0.0277-0.04940.2220.09650.2505-49.5735217.6647-22.4687
190.58540.17010.18140.60040.13810.4274-0.04330.02390.22720.0699-0.03150.01540.04750.0230.04210.1014-0.0126-0.03610.1174-0.01020.1426-48.429206.3037-11.5684
200.64030.0570.16890.47180.04470.4635-0.06650.098-0.0033-0.0737-0.00110.09890.0283-0.00070.01930.1552-0.02930.01460.1088-0.02140.0892-54.9429182.3926-19.6944
210.382-0.0382-0.02030.6250.03080.3761-0.05680.10450.0883-0.042-0.00050.07430.00670.01090.04320.0963-0.014-0.00840.1031-0.0050.1277-49.9422197.625-14.7325
221.2156-0.0649-0.01470.8462-0.21770.6441-0.06360.10470.0455-0.05640.0425-0.0503-0.069-0.0098-0.00690.1622-0.0417-0.02860.22980.16020.2358-51.4643139.1192-93.3009
230.45510.25510.08810.47540.08310.2356-0.06480.05620.07590.0260.00710.01770.00740.0150.05840.1429-0.0338-0.0190.15870.01030.1561-45.8241125.3636-83.9135
240.5913-0.05930.10250.41850.06690.3448-0.11470.205-0.0732-0.05190.0230.0692-0.02180.00790.01630.1393-0.07950.05810.174-0.0550.1285-53.6465101.8418-91.0308
250.1986-0.0037-0.10320.60440.08610.2411-0.08780.1322-0.02360.04740.02240.0671-0.0076-0.03250.03710.1066-0.04550.00440.1282-0.00650.1132-49.9247114.3705-84.5686
260.8856-0.15670.2460.1699-0.04460.37580.01240.04390.0368-0.0116-0.028-0.0383-0.03850.00210.00160.34270.1432-0.17770.38480.15550.5237-30.8022135.691310.955
270.1458-0.14590.16080.1489-0.14360.293-0.00030.14550.0999-0.0573-0.0246-0.0102-0.02940.05180.08470.19750.0014-0.19490.28030.15290.3558-18.5264124.013314.7351
280.24410.0840.00890.17930.07610.1906-0.06650.17830.14870.0039-0.03760.0169-0.0684-0.0209-0.10950.2020.0162-0.2330.16280.01160.3173-30.06120.497824.5355
290.6230.17690.42740.06230.06940.5186-0.11160.1591-0.0304-0.0941-0.0230.20620.038-0.02940.00710.1922-0.0156-0.05920.19-0.08360.2273-33.701297.388817.0043
300.55540.50120.55671.56930.71091.078-0.0395-0.0001-0.1470.06210.00670.0240.0988-0.0355-0.01090.1380.01040.00490.1091-0.0350.1723-23.490294.311125.3233
310.241-0.10290.01930.145-0.04670.1651-0.04870.1754-0.0271-0.1420.00420.08220.0057-0.0798-0.00970.2417-0.016-0.14660.2756-0.12920.1997-37.4215100.78384.0724
320.6170.251-0.06110.9430.16410.3234-0.06330.14440.05080.0246-0.16490.01-0.0523-0.0099-0.06740.17270.0052-0.13320.2046-0.00780.2756-30.1168111.164621.4933
330.1467-0.0972-0.01310.1879-0.08180.1867-0.03120.09060.12230.00310.0039-0.0087-0.0507-0.0507-0.00330.18050.0543-0.20080.22580.07180.3809-38.645126.771917.6998
340.82520.26880.68340.3006-0.04080.887-0.04890.12350.082-0.0113-0.04290.1854-0.0296-0.09250.00350.15730.0249-0.10490.1707-0.04660.2442-36.8292110.676320.8685
350.37270.28320.00281.25670.30250.5049-0.11720.158-0.0835-0.06550.0431-0.11470.00840.07250.02610.1680.017-0.03230.1756-0.0730.1665-15.917496.217620.665
360.92610.279-0.05370.2432-0.08350.34240.0438-0.0289-0.0493-0.02790.02690.0094-0.0179-0.0177-0.03280.62980.08950.21540.41480.3120.6652-50.4796155.854524.4143
370.18320.113-0.0590.4655-0.00880.2052-0.097-0.0923-0.18150.0636-0.0062-0.05220.10310.026-0.06180.6110.08560.23690.09550.0990.3156-50.0842176.113117.4093
380.3304-0.021-0.00380.4187-0.17510.3005-0.1556-0.1579-0.12270.30750.05760.05280.110.02370.03630.4430.05080.08710.11720.03040.1439-50.6315184.35418.5274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 135 )
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 265 )
4X-RAY DIFFRACTION4chain 'A' and (resid 266 through 387 )
5X-RAY DIFFRACTION5chain 'B' and (resid 15 through 52 )
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 135 )
7X-RAY DIFFRACTION7chain 'B' and (resid 136 through 265 )
8X-RAY DIFFRACTION8chain 'B' and (resid 266 through 317 )
9X-RAY DIFFRACTION9chain 'B' and (resid 318 through 387 )
10X-RAY DIFFRACTION10chain 'C' and (resid 15 through 52 )
11X-RAY DIFFRACTION11chain 'C' and (resid 53 through 129 )
12X-RAY DIFFRACTION12chain 'C' and (resid 130 through 265 )
13X-RAY DIFFRACTION13chain 'C' and (resid 266 through 387 )
14X-RAY DIFFRACTION14chain 'D' and (resid 15 through 42 )
15X-RAY DIFFRACTION15chain 'D' and (resid 43 through 135 )
16X-RAY DIFFRACTION16chain 'D' and (resid 136 through 250 )
17X-RAY DIFFRACTION17chain 'D' and (resid 251 through 387 )
18X-RAY DIFFRACTION18chain 'E' and (resid 15 through 66 )
19X-RAY DIFFRACTION19chain 'E' and (resid 67 through 135 )
20X-RAY DIFFRACTION20chain 'E' and (resid 136 through 265 )
21X-RAY DIFFRACTION21chain 'E' and (resid 266 through 387 )
22X-RAY DIFFRACTION22chain 'F' and (resid 15 through 52 )
23X-RAY DIFFRACTION23chain 'F' and (resid 53 through 135 )
24X-RAY DIFFRACTION24chain 'F' and (resid 136 through 250 )
25X-RAY DIFFRACTION25chain 'F' and (resid 251 through 387 )
26X-RAY DIFFRACTION26chain 'G' and (resid 15 through 52 )
27X-RAY DIFFRACTION27chain 'G' and (resid 53 through 87 )
28X-RAY DIFFRACTION28chain 'G' and (resid 88 through 135 )
29X-RAY DIFFRACTION29chain 'G' and (resid 136 through 182 )
30X-RAY DIFFRACTION30chain 'G' and (resid 183 through 206 )
31X-RAY DIFFRACTION31chain 'G' and (resid 207 through 250 )
32X-RAY DIFFRACTION32chain 'G' and (resid 251 through 283 )
33X-RAY DIFFRACTION33chain 'G' and (resid 284 through 321 )
34X-RAY DIFFRACTION34chain 'G' and (resid 322 through 346 )
35X-RAY DIFFRACTION35chain 'G' and (resid 347 through 387 )
36X-RAY DIFFRACTION36chain 'H' and (resid 15 through 56 )
37X-RAY DIFFRACTION37chain 'H' and (resid 57 through 162 )
38X-RAY DIFFRACTION38chain 'H' and (resid 163 through 387 )

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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