[English] 日本語
Yorodumi
- PDB-1rkm: STRUCTURE OF OPPA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rkm
TitleSTRUCTURE OF OPPA
ComponentsOLIGO-PEPTIDE BINDING PROTEIN
KeywordsBINDING PROTEIN / PEPTIDE TRANSPORT
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic oligopeptide-binding protein OppA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSleigh, S.H. / Tame, J.R.H. / Wilkinson, A.J.
Citation
Journal: Biochemistry / Year: 1997
Title: Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine.
Authors: Sleigh, S.H. / Tame, J.R. / Dodson, E.J. / Wilkinson, A.J.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: The Role of Water in Sequence-Independent Ligand Binding by an Oligopeptide Transporter Protein
Authors: Tame, J.R. / Sleigh, S.H. / Wilkinson, A.J. / Ladbury, J.E.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure Determination of Oppa at 2.3 Angstroms Resolution Using Multiple Wavelength Anomalous Methods
Authors: Glover, I.D. / Denny, R. / Nguti, N.D. / Mcsweeney, S. / Thompson, A. / Dodson, E. / Wilkinson, A.J. / Tame, J.R.H.
#3: Journal: Structure / Year: 1995
Title: The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands
Authors: Tame, J.R. / Dodson, E.J. / Murshudov, G. / Higgins, C.F. / Wilkinson, A.J.
#4: Journal: Science / Year: 1994
Title: The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein
Authors: Tame, J.R. / Murshudov, G.N. / Dodson, E.J. / Neil, T.K. / Dodson, G.G. / Higgins, C.F. / Wilkinson, A.J.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Jul 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Remark 700SHEET THE HELIX AND SHEET RECORDS PRESENTED HERE DIFFER FROM THE LIST THAT THE PDB HAS GENERATED ...SHEET THE HELIX AND SHEET RECORDS PRESENTED HERE DIFFER FROM THE LIST THAT THE PDB HAS GENERATED USING DSSP WHICH APPEAR ON ACTUAL HELIX AND SHEET RECORDS FURTHER DOWN IN THE ENTRY. BECAUSE OF LINE LENGTH LIMITATIONS THE FORMAT OF THE SHEET INFORMATION PRESENTED IN THIS REMARK HAS BEEN MODIFIED. HELIX 1 1 VAL A 34 LEU A 43 1 HELIX 2 2 HIS A 91 ALA A 101 1 HELIX 3 3 TYR A 112 GLY A 116 1 HELIX 4 4 ILE A 121 ALA A 126 1 HELIX 5 5 LYS A 169 PHE A 175 1 HELIX 6 6 GLU A 229 SER A 238 1 HELIX 7 7 ILE A 250 GLU A 259 1 HELIX 8 8 VAL A 287 ALA A 296 1 HELIX 9 9 ARG A 299 LYS A 305 1 HELIX 10 10 GLN A 337 ALA A 351 1 HELIX 11 11 ASP A 369 LEU A 386 1 HELIX 12 12 TRP A 397 GLN A 406 1 HELIX 13 13 THR A 424 LEU A 427 1 HELIX 14 14 PRO A 444 LYS A 455 1 HELIX 15 15 ASP A 459 ASP A 476 1 SH 1 A 7 VAL A 264 PRO A 268 0 SH 2 A 7 VAL A 486 LEU A 490 -1 N ARG A 489 O ARG A 265 SH 3 A 7 ASP A 242 TYR A 245 -1 N THR A 244 O LEU A 490 SH 4 A 7 THR A 14 ASN A 18 1 N ASN A 18 O MET A 243 SH 5 A 7 GLN A 220 LEU A 224 1 N GLN A 220 O LEU A 15 SH 6 A 7 ARG A 201 ARG A 206 -1 N LEU A 204 O VAL A 221 SH 7 A 7 TYR A 191 VAL A 197 -1 N VAL A 197 O ARG A 201 SH 1 B 4 ALA A 61 LYS A 67 0 SH 2 B 4 VAL A 71 LEU A 76 -1 N HIS A 75 O GLU A 62 SH 3 B 4 THR A 143 THR A 147 -1 N VAL A 146 O TRP A 72 SH 4 B 4 VAL A 136 ASP A 140 -1 N ASP A 140 O THR A 143 SH 1 C 5 ASN A 389 GLN A 395 0 SH 2 C 5 THR A 360 ASN A 366 1 O TYR A 365 N GLN A 395 SH 3 C 5 VAL A 411 CYS A 417 1 O VAL A 411 N LEU A 364 SH 4 C 5 CYS A 271 ILE A 277 -1 N GLU A 276 O ALA A 412 SH 5 C 5 ILE A 479 TYR A 484 -1 N TYR A 483 O TYR A 273

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OLIGO-PEPTIDE BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)58,8791
Polymers58,8791
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.840, 97.840, 137.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein OLIGO-PEPTIDE BINDING PROTEIN


Mass: 58878.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Description: THE OLIGOPEPTIDE BINDING PROTEIN OPPA IS SYNTHESISED AS A 542 AMINO ACID PRE-PROTEIN. THE 25 AMINO ACID SIGNAL PEPTIDE IS CLEAVED FROM THE N-TERMINUS TO GIVE A 517 RESIDUE MATURE PROTEIN ...Description: THE OLIGOPEPTIDE BINDING PROTEIN OPPA IS SYNTHESISED AS A 542 AMINO ACID PRE-PROTEIN. THE 25 AMINO ACID SIGNAL PEPTIDE IS CLEAVED FROM THE N-TERMINUS TO GIVE A 517 RESIDUE MATURE PROTEIN IN THE PERIPLASMIC SPACE. ALL 517 RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP.
References: UniProt: P06202
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.22 Å3/Da / Density % sol: 61.6 %
Crystal growpH: 7.5
Details: 3M (NH4)2SO4, 0.1M HEPES PH7.5, 0.2M NACL AND 20MG/ML OPPA
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 Mammonium sulfate1reservoir
20.3 M1reservoirNaCl
330 mg/mlprotein1drop
40.1 MHEPES1drop

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 30015 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.6 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 112007
Reflection shell
*PLUS
% possible obs: 99.5 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
AgrovataCCP4data reduction
AMoREphasing
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OLIGOPEPTIDE BINDING PROTEIN, PDB CODE 2OLB

2olb


Resolution: 2.4→20 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -5 %RANDOM
Rwork0.191 ---
obs-30015 99.3 %-
Displacement parametersBiso mean: 28.9 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4190 0 0 125 4315
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0490.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1062
X-RAY DIFFRACTIONp_mcangle_it3.1013
X-RAY DIFFRACTIONp_scbond_it2.9372
X-RAY DIFFRACTIONp_scangle_it4.3963
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.01640.015
X-RAY DIFFRACTIONp_singtor_nbd0.1940.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1820.3
X-RAY DIFFRACTIONp_planar_tor5.47
X-RAY DIFFRACTIONp_staggered_tor21.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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