[English] 日本語
Yorodumi
- PDB-1vpl: Crystal structure of ABC transporter ATP-binding protein (TM0544)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vpl
TitleCrystal structure of ABC transporter ATP-binding protein (TM0544) from Thermotoga maritima at 2.10 A resolution
ComponentsABC transporter, ATP-binding protein
KeywordsLYASE / TM0544 / ABC TRANSPORTER ATP-BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of ABC transporter ATP-binding protein (TM0544) from Thermotoga maritima at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8193
Polymers28,6271
Non-polymers1922
Water2,450136
1
A: ABC transporter, ATP-binding protein
hetero molecules

A: ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6386
Polymers57,2542
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)90.590, 90.590, 72.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

-
Components

#1: Protein ABC transporter, ATP-binding protein


Mass: 28627.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0544 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ14
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.98 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 2.1→39.23 Å / Num. obs: 20216 / % possible obs: 99.2 % / Redundancy: 8 % / Biso Wilson estimate: 36.34 Å2 / Rsym value: 0.119 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 1371 / Rsym value: 0.66 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JI0

1ji0


Resolution: 2.1→39.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.791 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21581 1030 5.1 %RANDOM
Rwork0.17139 ---
obs0.17372 19181 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.89 Å20 Å2
2--1.79 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 10 136 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221932
X-RAY DIFFRACTIONr_bond_other_d0.0010.021875
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9822602
X-RAY DIFFRACTIONr_angle_other_deg0.87534356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33823.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40615384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6351518
X-RAY DIFFRACTIONr_chiral_restr0.10.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.2120.2385
X-RAY DIFFRACTIONr_nbd_other0.1830.21987
X-RAY DIFFRACTIONr_nbtor_other0.0910.21196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.212
X-RAY DIFFRACTIONr_mcbond_it2.69831302
X-RAY DIFFRACTIONr_mcbond_other0.5723494
X-RAY DIFFRACTIONr_mcangle_it3.44551933
X-RAY DIFFRACTIONr_scbond_it6.9638791
X-RAY DIFFRACTIONr_scangle_it9.4911669
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 69 5.05 %
Rwork0.231 1297 -
Refinement TLS params.Method: refined / Origin x: 28.0603 Å / Origin y: 34.1259 Å / Origin z: 15.2603 Å
111213212223313233
T-0.2159 Å20.0511 Å2-0.0093 Å2--0.0782 Å20.0042 Å2---0.0785 Å2
L0.6622 °2-0.2421 °2-0.6643 °2-0.631 °20.164 °2--4.7684 °2
S0.0373 Å °0.0372 Å °0.0381 Å °-0.025 Å °0.0264 Å °0.0124 Å °0.0859 Å °0.1137 Å °-0.0638 Å °
Refinement TLS groupSelection: ALL

+
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