[English] 日本語
Yorodumi
- PDB-3g4r: Ligand migration and cavities within scapharca dimeric hemoglobin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g4r
TitleLigand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to HEME and dichloroethane bound to the XE4 cavity
ComponentsGlobin-1
KeywordsOXYGEN BINDING / OXYGEN TRANSPORT / ALLOSTERY / OXYGEN AFFINITY / CYTOPLASM / HEME / IRON / METAL-BINDING / OXYGEN STORAGE/TRANSPORT / Transport
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / 1,2-DICHLOROETHANE / PROTOPORPHYRIN IX CONTAINING FE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKnapp, J.E. / Pahl, R. / Cohen, J. / Nichols, J.C. / Schulten, K. / Gibson, Q.H. / Srajer, V. / Royer Jr., W.E.
CitationJournal: Structure / Year: 2009
Title: Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.
Authors: Knapp, J.E. / Pahl, R. / Cohen, J. / Nichols, J.C. / Schulten, K. / Gibson, Q.H. / Srajer, V. / Royer, W.E.
History
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Globin-1
B: Globin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4228
Polymers31,9352
Non-polymers1,4876
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-42 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.140, 43.940, 83.530
Angle α, β, γ (deg.)90.00, 121.89, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Globin-1 / Globin I / HbI / Dimeric hemoglobin


Mass: 15967.304 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Gene: HBI / Plasmid: pCS-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110LACIQL8 / References: UniProt: P02213
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-DCE / 1,2-DICHLOROETHANE / ETHYLENE DICHLORIDE


Mass: 98.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4Cl2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 7.5
Details: 1.5-2.5M PHOSPHATE BUFFER, PH 7.50, SMALL TUBES, TEMPERATURE 298K, Microbatch, temperature 296K

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 13, 2004 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 38142 / Num. obs: 35053 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 12.4
Reflection shellResolution: 1.6→1.65 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.37 / % possible all: 87.7

-
Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SDH

3sdh


Resolution: 1.6→15.1 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1181837.33 / 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
Rfree0.219 1744 5 %RANDOM
Rwork0.2 ---
obs0.2 35053 91.6 %-
all-38142 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.873 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20.71 Å2
2--2.48 Å20 Å2
3----4.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→15.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 106 177 2515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 1.6→1.69 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 272 5.4 %
Rwork0.31 4775 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param19x.hemetoph19x.heme
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4dichloroethane.paramdichloroethane.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://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