[English] 日本語
Yorodumi
- PDB-2q32: Crystal structure of human heme oxygenase-2 C127A (HO-2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q32
TitleCrystal structure of human heme oxygenase-2 C127A (HO-2)
ComponentsHeme oxygenase 2
KeywordsOXIDOREDUCTASE / HO-2 / HEME Oxygenase / Structural Genomics Medical Relevance / Structural Genomics Community Request / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / Heme degradation / RHOA GTPase cycle / specific granule membrane / Iron uptake and transport / Cytoprotection by HMOX1 / response to oxidative stress ...heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / Heme degradation / RHOA GTPase cycle / specific granule membrane / Iron uptake and transport / Cytoprotection by HMOX1 / response to oxidative stress / response to hypoxia / heme binding / Neutrophil degranulation / endoplasmic reticulum membrane / membrane / metal ion binding / plasma membrane
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBianchetti, C.M. / Bingman, C.A. / Bitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Comparison of Apo- and Heme-bound Crystal Structures of a Truncated Human Heme Oxygenase-2.
Authors: Bianchetti, C.M. / Yi, L. / Ragsdale, S.W. / Phillips Jr., G.N.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heme oxygenase 2
B: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2764
Polymers60,9832
Non-polymers1,2942
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.769, 86.017, 97.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETAA30 - 24030 - 240
2ALAALABB31 - 24031 - 240
DetailsThe biological unit is a dimer (chains A & B in ASU).

-
Components

#1: Protein Heme oxygenase 2 / HO-2


Mass: 30491.271 Da / Num. of mol.: 2 / Mutation: C127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Hs.284279, HMOX2, HO2 / Plasmid: pGEX 4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P30519, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100


Mass: 646.849 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein solution (5 mg/ml Protein, 0.050 M Potassium chloride, 0.005 M Tris-HCl pH 8.5) mixed in a 1.5:1 ratio with the well solution (40% PEG 1500, 0.20 M Potassium glutamate, 0.10 M ...Details: Protein solution (5 mg/ml Protein, 0.050 M Potassium chloride, 0.005 M Tris-HCl pH 8.5) mixed in a 1.5:1 ratio with the well solution (40% PEG 1500, 0.20 M Potassium glutamate, 0.10 M Triethanolamine, pH 8.5). Cryoprotected with well solution, VAPOR DIFUSSION, HANGING DROP, temperature 277K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→49.148 Å / Num. obs: 28128 / % possible obs: 95.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.082 / Χ2: 1.17 / Net I/σ(I): 13.505
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.3-2.383.90.6081.92922450.98378.2
2.38-2.485.40.57124881.01586.5
2.48-2.596.80.48327281.09494.5
2.59-2.737.70.37128781.08299.2
2.73-2.980.26629111.308100
2.9-3.128.10.18129021.424100
3.12-3.448.10.12129311.325100
3.44-3.9380.09829451.131100
3.93-4.957.90.06929741.101100
4.95-49.1487.60.03631261.01599.8

-
Phasing

Phasing MRRfactor: 0.478 / Cor.coef. Fo:Fc: 0.475
Highest resolutionLowest resolution
Rotation4 Å49.15 Å
Translation4 Å49.15 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N45

1n45


Resolution: 2.4→49.148 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.213 / SU B: 17.022 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.331 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1275 5.056 %RANDOM
Rwork0.201 ---
obs0.204 25217 98.431 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.622 Å2
Baniso -1Baniso -2Baniso -3
1--2.315 Å20 Å20 Å2
2---1.049 Å20 Å2
3---3.364 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 70 154 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223770
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9825072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1455447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6725.072207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94615689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5851521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022899
X-RAY DIFFRACTIONr_nbd_refined0.1980.21825
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.24
X-RAY DIFFRACTIONr_mcbond_it0.5141.52272
X-RAY DIFFRACTIONr_mcangle_it0.79923520
X-RAY DIFFRACTIONr_scbond_it1.23231688
X-RAY DIFFRACTIONr_scangle_it1.9664.51552
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1675 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.470.5
MEDIUM THERMAL0.632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4620.336820.2631552186487.661
2.462-2.530.363760.2641608179693.764
2.53-2.6030.406840.2511668179497.659
2.603-2.6830.281830.2521600169699.233
2.683-2.770.278800.25915891669100
2.77-2.8670.298780.2415331611100
2.867-2.9750.271890.23214621551100
2.975-3.0960.343760.22314241500100
3.096-3.2330.263870.213621449100
3.233-3.390.29700.20213061376100
3.39-3.5730.288710.19212581329100
3.573-3.7880.276660.18311951261100
3.788-4.0480.266660.17811081174100
4.048-4.370.153610.15810551116100
4.37-4.7840.214530.1719701023100
4.784-5.3420.195490.199879928100
5.342-6.1570.216430.229790833100
6.157-7.5120.21270.208694721100
7.512-10.5060.248200.159552572100
10.506-49.1480.301140.22333735698.596
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.38670.9854-0.14862.1547-0.36592.18970.0001-0.0481-0.15870.1784-0.02790.0297-0.0414-0.07590.0278-0.27010.0546-0.0441-0.2374-0.0422-0.177325.65821.81736.717
23.12480.77630.38174.5599-1.65894.44450.02180.00290.20040.1975-0.2365-0.7597-0.21250.88850.2147-0.14370.0096-0.0572-0.06560.0832-0.059849.690215.595629.4417
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA29 - 4229 - 42
21AA43 - 6243 - 62
31AA63 - 13363 - 133
41AA134 - 162134 - 162
51AA163 - 181163 - 181
61AA182 - 203182 - 203
71AA204 - 229204 - 229
81AA230 - 241230 - 241
92BB31 - 4331 - 43
102BB44 - 6544 - 65
112BB66 - 11566 - 115
122BB116 - 132116 - 132
132BB133 - 154133 - 154
142BB155 - 176155 - 176
152BB177 - 196177 - 196
162BB197 - 218197 - 218
172BB219 - 242219 - 242

+
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