[English] 日本語
Yorodumi
- PDB-4ywh: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ywh
TitleCRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM ACTINOBACILLUS SUCCINOGENES 130Z (Asuc_0499, TARGET EFI-511068) WITH BOUND D-XYLOSE
ComponentsABC TRANSPORTER SOLUTE BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


monosaccharide-transporting ATPase / D-xylose transmembrane transport / ABC-type monosaccharide transporter activity / monosaccharide binding / periplasmic space / hydrolase activity
Similarity search - Function
D-xylose ABC transporter, substrate-binding protein / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-xylopyranose / D-xylose ABC transporter, periplasmic substrate-binding protein
Similarity search - Component
Biological speciesActinobacillus succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM ACTINOBACILLUS SUCCINOGENES 130Z (Asuc_0499, TARGET EFI-511068) WITH BOUND D-XYLOSE
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_close_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_atom_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC TRANSPORTER SOLUTE BINDING PROTEIN
B: ABC TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5814
Polymers73,2802
Non-polymers3002
Water3,027168
1
A: ABC TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7902
Polymers36,6401
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7902
Polymers36,6401
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.796, 37.670, 105.336
Angle α, β, γ (deg.)90.000, 91.500, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ABC TRANSPORTER SOLUTE BINDING PROTEIN / D-xylose ABC transporter / periplasmic substrate-binding protein


Mass: 36640.211 Da / Num. of mol.: 2 / Fragment: UNP residues 24-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus succinogenes (strain ATCC 55618 / 130Z) (bacteria)
Strain: ATCC 55618 / 130Z / Gene: Asuc_0499 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A6VLM7, monosaccharide-transporting ATPase
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Xylose); Reservoir (MCSG1 G4)(0.2 M Potassium Sodium Tartrate, 20 %(w/v) PEG 3350); Cryoprotection (20% Ethylene Glycol, 80% Reservoir)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 11, 2015 / 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: 2.35→24.838 Å / Num. obs: 26617 / % possible obs: 97.6 % / Redundancy: 5 % / Biso Wilson estimate: 31.31 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.04 / Rrim(I) all: 0.093 / Χ2: 0.753 / Net I/av σ(I): 14.538 / Net I/σ(I): 9 / Num. measured all: 133133
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.393.90.7511900.7640.3990.8550.6289.7
2.39-2.434.30.60612590.8310.3150.6860.62896.3
2.43-2.484.60.50913260.9130.2540.5710.66496.5
2.48-2.534.70.43113180.9190.2110.4820.67196.8
2.53-2.594.80.37212750.930.1840.4170.69697
2.59-2.654.80.31413260.9520.1530.3510.70796.3
2.65-2.714.80.27413280.9520.1330.3060.73697.3
2.71-2.794.90.24212750.9560.1180.270.76196.4
2.79-2.874.90.213280.9640.0980.2240.77796.9
2.87-2.964.90.17412970.9720.0850.1950.80397.6
2.96-3.0750.1413110.9740.0680.1560.76797
3.07-3.1950.1213550.980.0580.1340.88198
3.19-3.335.10.09713250.9780.0480.1090.84798.4
3.33-3.515.20.07913680.9830.0390.0890.85299.5
3.51-3.735.30.07113780.9840.0340.0790.80199.9
3.73-4.025.50.0613440.990.0280.0660.715100
4.02-4.425.60.06113810.990.0290.0680.778100
4.42-5.065.50.06613870.990.0320.0731.027100
5.06-6.385.50.06114150.9870.0290.0680.719100
6.38-5005.30.04814310.9930.0220.0530.49997.7

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MA0

4ma0


Resolution: 2.35→24.838 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1209 4.7 %
Rwork0.1567 24491 -
obs0.1607 25700 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.08 Å2 / Biso mean: 41.2848 Å2 / Biso min: 12.1 Å2
Refinement stepCycle: final / Resolution: 2.35→24.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 20 168 4872
Biso mean--27.21 37.21 -
Num. residues----617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144756
X-RAY DIFFRACTIONf_angle_d1.416431
X-RAY DIFFRACTIONf_chiral_restr0.058763
X-RAY DIFFRACTIONf_plane_restr0.006836
X-RAY DIFFRACTIONf_dihedral_angle_d15.2761770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.42780.2846860.1921701X-RAY DIFFRACTION60
2.4278-2.53810.32641320.2092642X-RAY DIFFRACTION90
2.5381-2.67180.27971160.20512804X-RAY DIFFRACTION96
2.6718-2.8390.30581430.21262777X-RAY DIFFRACTION97
2.839-3.05780.31151330.20652816X-RAY DIFFRACTION97
3.0578-3.36490.27391430.17352867X-RAY DIFFRACTION98
3.3649-3.85020.22871410.14332913X-RAY DIFFRACTION100
3.8502-4.8450.18911560.10932932X-RAY DIFFRACTION100
4.845-24.83950.17931590.1293039X-RAY DIFFRACTION100
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)
12.361-0.0238-0.72791.48860.26981.96460.06460.23360.2412-0.08240.1098-0.1398-0.0149-0.0143-0.20430.2351-0.03640.04790.16630.00140.267723.2094-4.1353-16.4984
21.0202-0.416-0.28080.6295-0.05991.14570.02740.27350.1919-0.08030.08570.0589-0.0653-0.2806-0.08880.2368-0.06080.06610.2275-0.00260.242212.4794-7.6173-20.1307
31.2543-0.2867-0.37340.99110.50332.5052-0.1252-0.0928-0.12660.01340.2706-0.12750.13220.0272-0.13060.2447-0.03750.01660.18630.00690.204614.852-11.2778-2.0827
41.3873-0.4152-0.72861.04220.68942.3613-0.2013-0.3484-0.0440.12810.07070.23080.0579-0.40260.12110.21740.0424-0.00390.35780.0370.25588.6976-3.74179.7841
51.7703-0.22880.12711.2833-0.16040.9386-0.2279-0.42210.02620.18340.16060.0385-0.093-0.05710.02370.22640.0875-0.01440.3224-0.04170.182717.49435.25059.3583
61.8064-0.2675-0.19551.05240.51192.3934-0.0169-0.07240.02150.02650.1248-0.06590.2482-0.085-0.05660.2375-0.02550.01870.1832-0.01890.217223.7917-18.7098-10.9831
71.38420.7296-0.13733.446-0.8291.7168-0.0216-0.4302-0.09240.0727-0.0535-0.83850.08740.55380.08050.24310.0391-0.0530.3698-0.12110.442132.94422.62923.8922
84.54130.76221.25775.6618-5.21296.7503-0.0959-0.15190.4074-0.116-0.0339-0.1847-0.06210.0590.12251.10330.33710.24180.48480.15481.105934.429917.07961.3623
93.10580.01240.61791.8193-0.28081.9189-0.0262-0.18230.49980.17940.19990.2248-0.1417-0.3443-0.10050.18320.0122-0.02520.2707-0.01810.27411.22047.679955.2416
101.57970.39160.2581.5408-0.84082.1957-0.1153-0.22040.09630.04140.1250.06040.10360.011-0.00280.18440.01850.0040.1674-0.04620.216818.8713-0.724761.3963
112.71210.8781-1.16560.9764-1.27432.6682-0.15920.5837-0.0402-0.20920.28620.08640.15970.111-0.11480.2575-0.02860.01990.2786-0.06910.239731.29665.530835.1355
121.74770.7933-0.22250.5367-0.40470.7793-0.11540.203-0.1258-0.043-0.0201-0.0820.10570.12980.10220.20330.01310.01940.1823-0.03110.219936.25867.35240.2032
132.52150.4572-0.28060.60540.06380.7086-0.3150.52730.2976-0.23150.21030.08250.023-0.09320.12140.2303-0.0298-0.04960.21260.04150.195128.300816.295535.8197
141.74650.1515-0.50371.1491-0.01152.3521-0.0549-0.0633-0.0711-0.27760.12030.14490.6376-0.33610.00350.3216-0.105-0.02460.232-0.00070.274712.639-7.514350.7988
151.7205-0.24730.03013.8524-0.62143.09350.00830.64990.1309-0.58530.12190.9091-0.0705-0.6312-0.06470.2788-0.0161-0.13310.36240.0260.409912.330613.549833.1834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 54 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 95 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 158 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 207 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 266 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 305 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 331 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 332 through 332 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 54 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 55 through 128 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 129 through 158 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 159 through 207 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 208 through 266 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 267 through 305 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 306 through 331 )B0

+
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://pdbjlvh1.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