[English] 日本語
Yorodumi
- PDB-3lft: The Crystal Structure of the ABC domain in complex with L-Trp fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lft
TitleThe Crystal Structure of the ABC domain in complex with L-Trp from Streptococcus pneumonia to 1.35A
Componentsuncharacterized protein
Keywordsstructure genomics / unknown function / ABC / ATPase / cassette / L-Trp / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


ABC transporter, substrate-binding protein / ABC transporter substrate binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHAN / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.35 Å
AuthorsStein, A.J. / Mulligan, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: to be published
History
DepositionJan 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6294
Polymers62,2212
Non-polymers4082
Water9,746541
1
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3152
Polymers31,1101
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3152
Polymers31,1101
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.619, 68.630, 137.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein uncharacterized protein


Mass: 31110.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1069 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97QX5, UniProt: A0A0H2UPV6*PLUS
#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.1M Tris pH 8.5, 0.2M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 113883 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.095 / Χ2: 2.68 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.35-1.45.30.767112741.1011100
1.4-1.455.30.546112551.091100
1.45-1.525.30.382113161.1651100
1.52-1.65.40.269112781.2821100
1.6-1.75.40.209113021.5121100
1.7-1.835.40.156113441.912199.9
1.83-2.025.40.119113702.714199.9
2.02-2.315.40.101114203.916199.8
2.31-2.915.40.091114965.135199.9
2.91-505.30.07118286.743199.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.35→36.29 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.185 / SU B: 1.893 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5696 5 %RANDOM
Rwork0.182 ---
obs0.183 113740 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.264 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.35→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 30 541 4754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224402
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9816046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83327.737137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63515731
X-RAY DIFFRACTIONr_chiral_restr0.0880.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213218
X-RAY DIFFRACTIONr_mcbond_it0.5891.52981
X-RAY DIFFRACTIONr_mcangle_it1.00524847
X-RAY DIFFRACTIONr_scbond_it1.81531421
X-RAY DIFFRACTIONr_scangle_it2.7424.51174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.3850.3173870.2837713832197.344
1.385-1.4220.2823530.2477753812099.828
1.422-1.4640.2244040.2157536794999.887
1.464-1.5090.2324160.1937264768699.922
1.509-1.5580.214040.1777047745599.946
1.558-1.6120.2063340.176874721199.958
1.612-1.6730.2083510.1666594695299.899
1.673-1.7410.1923090.1646423673899.911
1.741-1.8190.1773240.1616142647099.938
1.819-1.9070.1823300.1645847618499.887
1.907-2.010.1962640.1725599587099.881
2.01-2.1320.1883000.185268557899.821
2.132-2.2780.192660.1715003527799.848
2.278-2.460.1822390.1784656489899.939
2.46-2.6930.2142570.194279454099.912
2.693-3.0090.2191990.1953933413999.831
3.009-3.4710.2141730.1813473365599.754
3.471-4.2410.1841490.1652983313599.904
4.241-5.9570.1881430.1772324247599.677
5.957-36.2890.221940.2241333148795.965
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)
11.7716-0.4773-0.10811.4548-0.09090.88730.06950.1378-0.0807-0.1296-0.06510.0550.0405-0.0396-0.00440.0698-0.0048-0.00930.0567-0.00280.0095.75432.3347-7.9787
215.0806-4.12881.04018.0549-0.39123.669-0.0920.0064-0.14190.06640.10880.6182-0.0208-0.194-0.01680.0596-0.0324-0.01420.07490.02430.0949-6.3827-0.0109-4.1795
39.01921.2064-0.07661.6745-0.22821.24520.02060.1762-0.1094-0.1838-0.040.11060.0892-0.15320.01940.148-0.006-0.00930.120.00030.05784.7345.8654-13.1603
45.9537-0.6397-0.58514.07960.02953.11840.01090.27530.1182-0.26680.04270.1156-0.0237-0.1354-0.05360.09160.0052-0.00020.07880.0440.03889.639915.754-14.174
51.238-0.1976-0.07211.2529-0.26820.72490.0140.03090.17850.01660.0153-0.0101-0.1197-0.0797-0.02930.06160.00970.00690.04650.01850.03967.225413.4638-3.2551
66.4346-0.7752-2.56944.50860.68763.22770.0427-0.13010.2433-0.044-0.0357-0.0259-0.29140.079-0.0070.087-0.0199-0.01640.0522-0.01040.051812.111615.46277.489
71.0707-0.5366-0.04031.375-0.05640.4701-0.0208-0.06430.08220.09110.0302-0.0483-0.08490.0066-0.00940.059-0.0006-0.00450.0350.00610.01228.74888.84037.8324
84.6656-2.24472.38738.6636-1.64833.3964-0.2694-0.5692-0.10280.84980.1710.0825-0.1284-0.20140.09840.11810.0184-0.00370.09270.02930.029520.5388-6.43314.8125
91.65250.2585-0.21731.4299-0.38111.42360.03-0.10150.00240.0619-0.105-0.21980.01360.17780.0750.0486-0.0074-0.01540.07830.02280.064627.5145-2.68157.0437
106.8577-3.03830.082614.6429-0.05979.3413-0.1114-0.37560.52110.2993-0.0108-0.2809-0.33570.30580.12220.0733-0.0318-0.0450.1093-0.03570.094426.03392.96212.4683
1110.00261.5641-3.58452.591-2.322111.6271-0.023-0.93280.22650.1183-0.0493-0.0719-0.20460.35620.07230.1039-0.0231-0.07050.17730.00980.105430.6562-2.075515.3276
121.6661-0.52970.41231.8819-0.76242.04370.08890.12810.0775-0.2231-0.1323-0.28780.03320.12260.04340.10660.00680.03410.15570.04610.141734.1761-0.5263-4.0025
131.5389-0.6278-0.00611.1344-0.00590.56670.09810.2217-0.0619-0.1507-0.1508-0.15360.11390.14090.05260.07330.03570.01680.10110.02890.076127.0457-7.4275-1.2658
143.5638-0.98591.91673.588-2.647710.40720.17650.2972-0.2611-0.3631-0.13660.10470.32440.0301-0.03990.08350.02680.00740.0423-0.01330.076421.2365-13.4547-0.702
155.0948-2.48381.70711.3846-0.95470.6965-0.0266-0.0354-0.19360.01810.0550.09340.024-0.0318-0.02840.06080.00160.00940.03820.00410.04817.3786-3.80113.0633
163.4613-1.7303-0.42714.80681.92512.8721-0.0227-0.1095-0.12160.0415-0.06570.1526-0.0755-0.18690.08840.05780.00320.01050.07120.01290.0507-5.51668.83011.1451
172.3071-1.50450.14114.5546-0.40091.9461-0.0663-0.05390.070.10410.06050.0291-0.0727-0.08160.00580.05250.0010.0040.04740.0060.00552.74659.52318.4831
185.2181-5.098-5.30799.92825.777212.45630.0568-0.095-0.30590.2529-0.0330.1082-0.1018-0.0908-0.02380.048-0.01830.00130.01930.01580.093215.3044-12.51117.5724
1915.0456-2.63572.55467.1114-0.71213.7909-0.1758-0.061-0.23350.07450.12170.12050.20330.09510.05410.12220.05330.02230.0769-0.00310.104826.3163-21.80762.7187
207.3018-3.19412.94023.4821-0.97934.4825-0.0269-0.2691-0.37120.2350.06220.12840.24580.067-0.03530.134-0.02730.00830.07220.03160.140617.6185-19.85449.7188
211.61661.5424-0.98896.3988-1.70932.48230.00290.06250.19830.45140.41230.737-0.1712-0.3022-0.41520.0970.06720.06740.1880.11960.1505-19.1124-8.039238.0639
223.7512-2.79960.76024.352-1.79751.8399-0.0831-0.247-0.2089-0.12-0.15390.4350.3767-0.49030.2370.1829-0.04180.11140.54030.03090.4764-32.4517-8.541437.3978
2323.26071.5371-3.67368.845-1.86485.16370.2872-0.67490.20551.0320.07620.3001-0.3696-0.2911-0.36340.25840.08020.04810.18720.06920.0763-15.8047-12.007344.7844
244.6771-2.79562.20562.5129-3.00491.9923-0.1947-0.317-0.08090.36890.22120.005-0.3099-0.1874-0.02650.26140.047-0.00460.21520.06480.1631-11.6156-19.173644.5295
2515.25810.77457.1066.9824-3.617510.4551-0.0084-0.4142-0.30440.76190.3781.04290.3753-0.6045-0.36950.2952-0.00980.15440.24750.1480.3151-24.8175-22.724643.0279
262.81661.1952-0.95916.14-2.12662.0934-0.20210.0848-0.16960.01680.46240.3340.3293-0.283-0.26030.1094-0.0212-0.02470.13940.08460.0915-17.4757-20.132635.705
271.97010.1772-1.17574.6021-3.20922.9037-0.3920.3197-0.1646-0.78111.01260.63060.7819-0.5664-0.62060.2501-0.1607-0.13110.37180.05880.342-18.8395-19.03829.4738
282.0446-0.73341.78220.68360.28092.56570.35550.3014-0.333-0.2-0.03730.10010.45220.1494-0.31820.4279-0.1538-0.09210.34150.08290.2913-18.7249-22.443723.9898
292.28941.721-1.06653.0425-2.2212.3906-0.09630.1348-0.0295-0.31510.22010.08980.2347-0.2706-0.12380.1038-0.0148-0.01980.06760.01480.0199-5.7556-1.123218.0131
301.61190.4122-0.72561.9938-1.62262.8184-0.0964-0.0943-0.2349-0.1535-0.0087-0.19190.2739-0.05960.10510.11050.0007-0.00020.0580.02440.0534-0.0703-8.774625.196
315.83862.5532-3.38728.68780.52868.3464-0.19260.0741-0.3155-0.13050.015-0.01130.4619-0.09130.17770.1505-0.01840.03250.04780.00010.05351.3971-7.464513.5468
321.74350.34370.345.3125-11.534225.2589-0.1744-0.0276-0.2986-0.2524-0.1874-0.26780.43090.4120.36170.16060.03630.02660.07970.0070.10947.1802-5.720320.0554
332.2560.5289-1.52353.3948-1.3942.6395-0.0182-0.1869-0.04210.2203-0.0878-0.2872-0.03850.18170.1060.12250.0001-0.04780.1330.04790.08346.6533-5.551235.5577
341.0720.670.09342.1174-0.71241.05290.0658-0.23080.03050.1983-0.0326-0.0059-0.099-0.0869-0.03320.089-0.0017-0.00870.09640.00990.029-1.78831.715730.8447
358.46537.1648-3.31459.0199-3.86489.258-0.028-0.05980.0833-0.37450.73471.0456-0.2393-0.4788-0.70670.074-0.0349-0.0790.30350.28130.3736-22.5743-4.509828.2878
365.27819.4873-4.4349.7567-0.601718.3707-0.48850.29670.3447-0.9770.39550.8584-0.46650.26020.0930.1999-0.1384-0.27970.36670.39270.7237-30.5184-13.470229.3516
373.81163.88790.20469.3194-0.1651.29340.0495-0.0185-0.1752-0.36290.00650.15550.2133-0.1504-0.0560.1678-0.0646-0.11820.22180.10680.176-22.5046-15.508721.2729
383.96156.03333.970610.49044.42955.5802-0.1138-0.13370.3673-0.1489-0.04310.6485-0.1674-0.23470.15690.08030.02990.00170.1171-0.03010.1612-9.52839.355624.4498
392.5742-0.1431.16980.2901-0.4263.33620.1030.10110.0310.00180.04880.0458-0.11950.0349-0.15180.12970.0236-0.00460.0595-0.01580.0454-3.259214.31920.8899
400.6999-1.17522.03412.2415-3.455314.68730.0567-0.1881-0.078-0.05180.36450.14780.3826-0.1756-0.42120.12270.0108-0.02230.15210.01350.1456-12.693410.946219.5307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 71
2X-RAY DIFFRACTION2A72 - 80
3X-RAY DIFFRACTION3A81 - 96
4X-RAY DIFFRACTION4A97 - 109
5X-RAY DIFFRACTION5A110 - 141
6X-RAY DIFFRACTION6A142 - 150
7X-RAY DIFFRACTION7A151 - 167
8X-RAY DIFFRACTION8A168 - 172
9X-RAY DIFFRACTION9A173 - 199
10X-RAY DIFFRACTION10A200 - 204
11X-RAY DIFFRACTION11A205 - 214
12X-RAY DIFFRACTION12A215 - 234
13X-RAY DIFFRACTION13A235 - 271
14X-RAY DIFFRACTION14A272 - 278
15X-RAY DIFFRACTION15A279 - 292
16X-RAY DIFFRACTION16A293 - 302
17X-RAY DIFFRACTION17A303 - 313
18X-RAY DIFFRACTION18A314 - 320
19X-RAY DIFFRACTION19A321 - 329
20X-RAY DIFFRACTION20A330 - 343
21X-RAY DIFFRACTION21B52 - 71
22X-RAY DIFFRACTION22B72 - 88
23X-RAY DIFFRACTION23B89 - 94
24X-RAY DIFFRACTION24B95 - 103
25X-RAY DIFFRACTION25B104 - 113
26X-RAY DIFFRACTION26B114 - 130
27X-RAY DIFFRACTION27B131 - 143
28X-RAY DIFFRACTION28B144 - 161
29X-RAY DIFFRACTION29B162 - 179
30X-RAY DIFFRACTION30B180 - 202
31X-RAY DIFFRACTION31B203 - 209
32X-RAY DIFFRACTION32B210 - 215
33X-RAY DIFFRACTION33B216 - 234
34X-RAY DIFFRACTION34B235 - 281
35X-RAY DIFFRACTION35B282 - 292
36X-RAY DIFFRACTION36B293 - 297
37X-RAY DIFFRACTION37B304 - 314
38X-RAY DIFFRACTION38B315 - 322
39X-RAY DIFFRACTION39B323 - 336
40X-RAY DIFFRACTION40B337 - 343

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
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

Read more