[English] 日本語
Yorodumi
- PDB-2r79: Crystal Structure of a Periplasmic Heme Binding Protein from Pseu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r79
TitleCrystal Structure of a Periplasmic Heme Binding Protein from Pseudomonas aeruginosa
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / heme transport
Function / homology
Function and homology information


ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Periplasmic binding protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsHo, W.W. / Li, H. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins.
Authors: Ho, W.W. / Li, H. / Eakanunkul, S. / Tong, Y. / Wilks, A. / Guo, M. / Poulos, T.L.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5876
Polymers29,5951
Non-polymers9935
Water2,846158
1
A: Periplasmic binding protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)183,52536
Polymers177,5686
Non-polymers5,95730
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
crystal symmetry operation10_774-y+2,-x+2,-z-1/21
crystal symmetry operation11_754-x+y+2,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area24130 Å2
ΔGint-253 kcal/mol
Surface area61010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.913, 132.913, 72.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein Periplasmic binding protein


Mass: 29594.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 from ATCC / Plasmid: pET 101/D-TOPO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O68879
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 0.25M sodium chloride, 1.8M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL1-511
SYNCHROTRONSSRL BL1-521.74, 1.65
SYNCHROTRONSSRL BL1-531.74, 1.65
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMar 23, 2007mirrors
ADSC QUANTUM 42CCDMar 23, 2007mirrors
ADSC QUANTUM 43CCDMar 24, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray2
3GRAPHITEMADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.741
31.651
ReflectionResolution: 2.4→50 Å / Num. obs: 15023 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 24.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 735 / Rsym value: 0.53 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→43.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3016812.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1476 9.8 %RANDOM
Rwork0.193 ---
obs0.193 15013 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.2989 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.35 Å20 Å20 Å2
2--4.35 Å20 Å2
3----8.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 65 158 2279
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 221 9.1 %
Rwork0.223 2219 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param19x.heme2water.top
X-RAY DIFFRACTION3water_rep.paramtoph19x.heme2
X-RAY DIFFRACTION4hetero.parhetero.top

+
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