[English] 日本語
Yorodumi
- PDB-1qhu: MAMMALIAN BLOOD SERUM HAEMOPEXIN DEGLYCOSYLATED AND IN COMPLEX WI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qhu
TitleMAMMALIAN BLOOD SERUM HAEMOPEXIN DEGLYCOSYLATED AND IN COMPLEX WITH ITS LIGAND HAEM
ComponentsPROTEIN (HEMOPEXIN)
KeywordsBINDING PROTEIN / BETA PROPELLER / HAEM BINDING AND TRANSPORT / IRON METABOLISM
Function / homology
Function and homology information


heme transmembrane transporter activity / intracellular iron ion homeostasis / heme binding / extracellular region / metal ion binding
Similarity search - Function
Hemopexin / 4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Hemopexin / 4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Hemopexin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPaoli, M. / Baker, H.M. / Morgan, W.T. / Smith, A. / Baker, E.N.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of hemopexin reveals a novel high-affinity heme site formed between two beta-propeller domains.
Authors: Paoli, M. / Anderson, B.F. / Baker, H.M. / Morgan, W.T. / Smith, A. / Baker, E.N.
History
DepositionMay 27, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (HEMOPEXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7079
Polymers51,8321
Non-polymers8748
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.680, 61.950, 83.290
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (HEMOPEXIN)


Mass: 51832.293 Da / Num. of mol.: 1 / Fragment: BETA-PROPELLER DOMAIN / Source method: isolated from a natural source
Details: COVALENT LINK BETWEEN FE OF HAEM LIGAND AND I) NE2 OF HIS 213 AND II) NE2 OF HIS 265
Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: BLOOD SERUM / References: UniProt: P20058

-
Non-polymers , 5 types, 218 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsPROTEIN WAS DEGLYSOSYLATED PRIOR TO CRYSTALLISATION
Nonpolymer detailsLIGAND COMPLEXED TO HAEMOPEXIN ION BOUND IN THE CENTRAL TUNNEL OF THE C-TERMINAL DOMAIN IONS BOUND ...LIGAND COMPLEXED TO HAEMOPEXIN ION BOUND IN THE CENTRAL TUNNEL OF THE C-TERMINAL DOMAIN IONS BOUND IN THE CENTRAL TUNNEL ION BOUND IN THE CENTRAL TUNNEL
Sequence detailsN-TERMINUS IS DISORDERED IN ELECTRON DENSITY MAPS NUMERING OF RESIDUES IS SUCH THAT IT IS ...N-TERMINUS IS DISORDERED IN ELECTRON DENSITY MAPS NUMERING OF RESIDUES IS SUCH THAT IT IS CONSISTENT WITH THE RESIDUE NUMERING IN PDB ENTRY PDB1HXN.ENT FOR THE C-TERMINAL DOMAIN STRUCTURE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35 %
Crystal growpH: 7.5
Details: HANGING DROP, 4 DEGREES CENTIGRADES, RESEVOIR SOLUTION: 19-22% PEG 4000, 0.05 M TRIS HCL PH 7.5, 0.05-0.5 M EDTA, 0.2 NACL PROTEIN COMPLEX SOLUTION: 40 MG/ ML IN 0.05 M TRIS PH 7.0 AND 0.2 M NACL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
119-22 %(w/v)PEG40001reservoir
20.05 MTris-HCl1reservoir
30.05-0.5 MEDTA1reservoir
40.2 M1reservoirNaCl
540 mg/mlprotain1drop
60.05 MTris-HCl1drop
70.2 M1dropNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: CYCLINDRICALLY BENT TRIANGULAR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 19233 / % possible obs: 94.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.1 / % possible all: 77
Reflection
*PLUS
Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 77 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4AGROVATA-ROTAVATAdata reduction
AMoREphasing
MAMAmodel building
MAVEmodel building
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
MAMAphasing
MAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HXN AND 1FBL

1hxn

1fbl


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.5 / ESU R: 1.29 / ESU R Free: 0.33
Details: ELECTRON DENSITY FOR RESIDUES ARG 214, SER 215 AND HIS 222 IS POORLY DEFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 951 5 %RANDOM
Rwork0.207 ---
obs0.201 19233 94.7 %-
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 54 210 3463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0941.5
X-RAY DIFFRACTIONp_mcangle_it1.8392
X-RAY DIFFRACTIONp_scbond_it1.6972
X-RAY DIFFRACTIONp_scangle_it2.5062.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2110.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor17.720
X-RAY DIFFRACTIONp_staggered_tor23.830
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2750
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2.5 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35 Å2

+
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