[English] 日本語
Yorodumi
- PDB-7v5p: The dimeric structure of G80A/H81A myoglobin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v5p
TitleThe dimeric structure of G80A/H81A myoglobin
ComponentsMyoglobin
KeywordsOXYGEN BINDING / OXYGEN STORAGE
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsXie, C. / Nagao, S. / Shibata, N. / Higuchi, Y. / Hirota, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H02060 Japan
Japan Society for the Promotion of Science (JSPS)JP19K05695 Japan
Japan Science and TechnologyJP20338388 Japan
CitationJournal: Rsc Adv / Year: 2021
Title: Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region.
Authors: Xie, C. / Shimoyama, H. / Yamanaka, M. / Nagao, S. / Komori, H. / Shibata, N. / Higuchi, Y. / Shigeta, Y. / Hirota, S.
History
DepositionAug 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1266
Polymers33,8612
Non-polymers1,2654
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-97 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.527, 62.735, 83.355
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Myoglobin /


Mass: 16930.471 Da / Num. of mol.: 2 / Mutation: G80A, H81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium acetate, 0.1 M Tris-HCl, 10% (w/v) PEG 6,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→47.35 Å / Num. obs: 101566 / % possible obs: 97 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 23.1
Reflection shellResolution: 1.16→1.18 Å / Num. unique obs: 4675 / CC1/2: 0.893

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VM9
Resolution: 1.16→41.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.923 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20562 5098 5 %RANDOM
Rwork0.19651 ---
obs0.19697 96318 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.16→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 88 316 2794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132542
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172436
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.6963446
X-RAY DIFFRACTIONr_angle_other_deg1.4821.6215634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8365304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90524.63108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40615456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.678154
X-RAY DIFFRACTIONr_chiral_restr0.0720.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022854
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02538
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4573 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 379 -
Rwork0.245 6650 -
obs--91.89 %
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)
11.30072.844-1.15816.511-3.62795.40650.00060.02910.01590.02060.10130.0729-0.2387-0.2534-0.10190.0910.0674-0.01480.05690.0030.0316-0.86938.8122-4.9498
23.0601-0.20530.88170.7245-0.16191.69550.0064-0.1207-0.0247-0.0679-0.00780.03790.1527-0.11940.00150.04090.00270.02640.03140.00610.04497.2433-0.67111.0598
32.33692.8365-1.87785.9844-3.845.46430.0076-0.2224-0.06270.1747-0.1754-0.1782-0.07850.32610.16770.03480.01220.01010.06230.01120.031210.55212.481123.0133
40.3956-0.33570.20764.0146-2.8382.916-0.0283-0.0243-0.02-0.0137-0.0017-0.02380.1014-0.0490.030.02240.00060.01390.05030.00080.05541.64947.6899.3488
50.67270.2483-0.40822.23650.41413.2196-0.04830.00340.0018-0.22710.0002-0.09020.19250.19980.04810.0627-0.00880.02650.0534-0.00040.01746.146436.4857-12.7939
66.0056-2.5608-3.12623.73062.44985.6179-0.1272-0.44660.11460.13270.18910.106-0.153-0.0946-0.06190.04530.01150.00420.0841-0.00010.017-3.682546.91192.7961
71.7208-1.1425-2.04222.93921.76824.63070.0172-0.05890.0323-0.0191-0.0073-0.082-0.05590.095-0.00990.0256-0.0199-0.00590.0626-0.00040.02874.17736.59982.7636
88.6845-0.4162-0.324114.1523-2.71430.5463-0.0283-0.0112-0.3710.3699-0.2066-1.0988-0.0250.05610.23490.30630.0980.00760.09240.02130.109512.697429.8798-12.2882
91.9007-1.31071.7322.9062-1.16951.97520.0362-0.06090.00910.0052-0.0491-0.05790.1056-0.02270.01290.0444-0.03420.01350.0701-0.00740.01-3.693734.24158.9514
102.81531.4055-0.9442.5362-0.24891.4898-0.0052-0.040.1807-0.17080.04450.1268-0.0535-0.0119-0.03940.0412-0.0244-0.01850.02530.00420.0292-4.805646.7576-6.4527
113.0935-4.54751.2137.457-0.56635.29190.04750.07570.0405-0.138-0.04340.0377-0.4340.0678-0.00410.2056-0.02230.01930.01360.01260.0234-0.776448.2224-19.8778
123.98521.4739-0.303610.9815-2.96893.65410.11680.0158-0.0013-0.2012-0.00390.4226-0.174-0.2326-0.11280.0880.0099-0.03230.04720.02580.0451-9.613750.5453-14.4713
130.8058-1.09741.24053.0034-2.03392.5711-0.0483-0.0214-0.04140.00020.04520.02810.02440.09190.00310.02640.00980.00120.03890.02160.0379-3.512130.3363-0.9332
144.3094-3.0241.13144.9474-1.70084.6846-0.2559-0.18030.17920.51590.154-0.2144-0.3358-0.14070.10190.07170.0139-0.0310.0269-0.02430.03879.097717.543317.1562
151.02510.23790.67181.77910.38421.40130.02290.0682-0.1005-0.2646-0.0262-0.0973-0.0250.00350.00330.04690.01490.01780.0366-0.00950.05188.763.65940.4591
161.88991.08461.18144.03780.57712.77340.0003-0.07090.0856-0.0319-0.1109-0.3467-0.20320.04450.11060.028-0.00150.00940.01930.0110.070813.006219.13817.4266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2A19 - 39
3X-RAY DIFFRACTION3A40 - 49
4X-RAY DIFFRACTION4A50 - 87
5X-RAY DIFFRACTION5A88 - 106
6X-RAY DIFFRACTION6A107 - 122
7X-RAY DIFFRACTION7A123 - 145
8X-RAY DIFFRACTION8A146 - 153
9X-RAY DIFFRACTION9B1 - 15
10X-RAY DIFFRACTION10B16 - 39
11X-RAY DIFFRACTION11B40 - 50
12X-RAY DIFFRACTION12B51 - 63
13X-RAY DIFFRACTION13B64 - 86
14X-RAY DIFFRACTION14B87 - 99
15X-RAY DIFFRACTION15B100 - 133
16X-RAY DIFFRACTION16B134 - 153

+
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