[English] 日本語
Yorodumi
- PDB-1v8x: Crystal Structure of the Dioxygen-bound Heme Oxygenase from Coryn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v8x
TitleCrystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae
ComponentsHeme oxygenase
KeywordsOXIDOREDUCTASE / PROTEIN-HEME COMPLEX / HELIX / OXY
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / metal ion binding
Similarity search - Function
Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
sucrose / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Heme oxygenase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsUnno, M. / Matsui, T. / Chu, G.C. / Couture, M. / Yoshida, T. / Rousseau, D.L. / Olson, J.S. / Ikeda-Saito, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae: IMPLICATIONS FOR HEME OXYGENASE FUNCTION.
Authors: Unno, M. / Matsui, T. / Chu, G.C. / Couture, M. / Yoshida, T. / Rousseau, D.L. / Olson, J.S. / Ikeda-Saito, M.
History
DepositionJan 15, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heme oxygenase
B: Heme oxygenase
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,95122
Polymers72,5103
Non-polymers3,44119
Water8,089449
1
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4497
Polymers24,1701
Non-polymers1,2796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2037
Polymers24,1701
Non-polymers1,0336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2998
Polymers24,1701
Non-polymers1,1297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.003, 62.969, 107.490
Angle α, β, γ (deg.)90.00, 100.96, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 4 molecules ABC

#1: Protein Heme oxygenase /


Mass: 24170.158 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: PMW172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P71119, heme oxygenase (biliverdin-producing)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 467 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THE DEPOSITORS BELIEVE THAT ...THERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THE DEPOSITORS BELIEVE THAT THESE RESIDUES ARE CORRECT AND THERE ARE IN JOURNAL OF BACTERIOLOGY, VOL.179, PAGE 838-845 (1997), SCHMITT, M.P.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 50.292557 %
Crystal growTemperature: 303 K / Method: vapor diffusion / pH: 6.1
Details: MES, Ammonium sulfate, pH 6.1, VAPOR DIFFUSION, temperature 303K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 25, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 60634 / Num. obs: 60627 / % possible obs: 100 % / Redundancy: 3.8 % / Rsym value: 0.071 / Net I/σ(I): 22
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.343 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.46 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19252 6150 10.1 %RANDOM
Rwork0.15302 ---
all0.15703 ---
obs0.15705 54446 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.38 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 218 449 5679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215334
X-RAY DIFFRACTIONr_bond_other_d0.0040.024705
X-RAY DIFFRACTIONr_angle_refined_deg1.7812.047251
X-RAY DIFFRACTIONr_angle_other_deg1.264310877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9735624
X-RAY DIFFRACTIONr_chiral_restr0.1110.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025925
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021097
X-RAY DIFFRACTIONr_nbd_refined0.2310.21286
X-RAY DIFFRACTIONr_nbd_other0.2510.25478
X-RAY DIFFRACTIONr_nbtor_other0.090.22854
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2333
X-RAY DIFFRACTIONr_metal_ion_refined0.1090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.228
X-RAY DIFFRACTIONr_mcbond_it1.0691.53106
X-RAY DIFFRACTIONr_mcangle_it1.91624933
X-RAY DIFFRACTIONr_scbond_it3.09232228
X-RAY DIFFRACTIONr_scangle_it4.8714.52318
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 408
Rwork0.184 3984
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.96430.32210.48181.58490.06291.01810.0967-0.0218-0.04950.0141-0.0486-0.0260.035-0.0234-0.04810.10150.0091-0.02740.0327-0.01120.066823.7940.493-0.208
21.07270.2459-0.24140.73050.06720.8808-0.02440.0099-0.0079-0.07960.04510.0069-0.0216-0.0096-0.02070.06220.00290.00250.10560.01990.06097.6115.85527.04
31.1116-0.2203-0.23880.5128-0.4251.0912-0.1173-0.1698-0.11140.0713-0.0474-0.08960.00910.08140.16470.05150.0110.00190.13340.05740.085628.9995.48151.543
43.2792-4.1748-0.23451.3186-0.72721.9850.10610.1087-0.5872-0.1022-0.2062-0.00050.5-0.18680.10010.1887-0.0058-0.02790.0744-0.05530.193924.604-9.3660.615
514.9537.2485-1.465616.17141.67212.67770.1731.00340.589-0.3879-0.0882-0.472-0.3930.3785-0.08480.06090.03130.03450.16590.10520.07735.54118.84617.861
64.36452.4755-2.756713.8273-4.518815.81280.2769-0.26640.0660.566-0.61320.00240.10180.24860.33640.0824-0.01760.01290.15410.03540.083131.1911.17860.004
70000000000000000.1424000.142400.142424.041-8.004-1.2
80000000000000000.1424000.142400.14247.84918.2719.257
90000000000000000.1424000.142400.142428.8021.55258.836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2137 - 213
2X-RAY DIFFRACTION2BB307 - 5137 - 213
3X-RAY DIFFRACTION3CC607 - 8137 - 213
4X-RAY DIFFRACTION4AQ9011
5X-RAY DIFFRACTION5BS9021
6X-RAY DIFFRACTION6CU9031
7X-RAY DIFFRACTION7AR50011
8X-RAY DIFFRACTION8BT50021
9X-RAY DIFFRACTION9CV50031

+
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