[English] 日本語
Yorodumi
- PDB-3nnd: The crystal structure of ABC transporter from Rhodopseudomonas pa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nnd
TitleThe crystal structure of ABC transporter from Rhodopseudomonas palustris
ComponentsPossible substrate binding protein of ABC transporter system
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / ABC transporter / SGX
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
: / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Possible substrate binding protein of ABC transporter system
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of ABC transporter from Rhodopseudomonas palustris
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Possible substrate binding protein of ABC transporter system
A: Possible substrate binding protein of ABC transporter system
C: Possible substrate binding protein of ABC transporter system
D: Possible substrate binding protein of ABC transporter system


Theoretical massNumber of molelcules
Total (without water)161,4324
Polymers161,4324
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Possible substrate binding protein of ABC transporter system
A: Possible substrate binding protein of ABC transporter system


Theoretical massNumber of molelcules
Total (without water)80,7162
Polymers80,7162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-47 kcal/mol
Surface area30390 Å2
MethodPISA
3
C: Possible substrate binding protein of ABC transporter system
D: Possible substrate binding protein of ABC transporter system


Theoretical massNumber of molelcules
Total (without water)80,7162
Polymers80,7162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-46 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.742, 118.427, 93.464
Angle α, β, γ (deg.)90.00, 106.87, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Possible substrate binding protein of ABC transporter system


Mass: 40358.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA4397 / Plasmid: Codon+ril Stratagene / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) / References: UniProt: Q6N1K8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 291 K / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→118.43 Å / Num. obs: 40725 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 56.58 Å2 / Rmerge(I) obs: 0.111
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.486 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→51.54 Å / SU ML: 0.51 / σ(F): 0.03 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.296 2019 4.96 %
Rwork0.244 --
obs0.246 40725 98.1 %
all-41463 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.84 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.2227 Å2-0 Å23.0359 Å2
2--1.4897 Å2-0 Å2
3---6.733 Å2
Refinement stepCycle: LAST / Resolution: 2.8→51.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10115 0 0 140 10255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710335
X-RAY DIFFRACTIONf_angle_d1.11413974
X-RAY DIFFRACTIONf_dihedral_angle_d19.0583724
X-RAY DIFFRACTIONf_chiral_restr0.0721594
X-RAY DIFFRACTIONf_plane_restr0.0061775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.31911220.26182683X-RAY DIFFRACTION94
2.87-2.94760.3791270.27242640X-RAY DIFFRACTION95
2.9476-3.03430.35031260.27442746X-RAY DIFFRACTION97
3.0343-3.13230.35961460.26922727X-RAY DIFFRACTION98
3.1323-3.24420.32791440.26142747X-RAY DIFFRACTION98
3.2442-3.37410.31051410.24782785X-RAY DIFFRACTION98
3.3741-3.52760.34311420.25232759X-RAY DIFFRACTION99
3.5276-3.71350.28481690.23122762X-RAY DIFFRACTION99
3.7135-3.94610.28131470.21872800X-RAY DIFFRACTION99
3.9461-4.25070.24731560.21892809X-RAY DIFFRACTION99
4.2507-4.67820.24921570.20792766X-RAY DIFFRACTION99
4.6782-5.35450.25181490.21472807X-RAY DIFFRACTION99
5.3545-6.74370.29331440.24792828X-RAY DIFFRACTION99
6.7437-51.54760.28891490.24882847X-RAY DIFFRACTION99

+
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