[English] 日本語
Yorodumi
- PDB-1mz0: STRUCTURE OF MYOGLOBIN MB-YQR 316 ns AFTER PHOTOLYSIS OF CARBON M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mz0
TitleSTRUCTURE OF MYOGLOBIN MB-YQR 316 ns AFTER PHOTOLYSIS OF CARBON MONOXIDE SOLVED FROM LAUE DATA AT RT.
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE / CO COMPLEX / RESPIRATORY PROTEIN / HEME / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body from starting model. / Resolution: 1.6 Å
AuthorsBourgeois, D. / Vallone, B. / Schotte, F. / Arcovito, A. / Miele, A.E. / Sciara, G. / Wulff, M. / Anfinrud, P. / Brunori, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography.
Authors: Bourgeois, D. / Vallone, B. / Schotte, F. / Arcovito, A. / Miele, A.E. / Sciara, G. / Wulff, M. / Anfinrud, P. / Brunori, M.
#1: Journal: Biophys.J. / Year: 1999
Title: Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10)
Authors: Brunori, M. / Cutruzzol, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin.
Authors: Brunori, M. / Vallone, B. / Cutruzzol, F. / Travaglini-Allocatelli, C. / Berendzen, J. / Chu, K. / Sweet, R.M. / Schlichting, I.
History
DepositionOct 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Version format compliance
Revision 1.4Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2985
Polymers17,4611
Non-polymers8374
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.200, 91.200, 45.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Number of models2
Components on special symmetry positions
IDModelComponents
11A-501-

SO4

21A-501-

SO4

32A-501-

SO4

42A-501-

SO4

DetailsThe biological assembly is the content of the asymmetric unit. Two states are described: chain A (0.82 occupancy) corresponds to the part of the molecules in the crystal which are in the dark state; chain B (occupancy 0.18) corresponds to the part of the molecules in the crystal which are in the light state.

-
Components

#1: Protein Myoglobin /


Mass: 17461.250 Da / Num. of mol.: 1 / Mutation: L29Y, H64Q, T67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: pUC91 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / Keywords: L29(B10)Y, H64(E7)Q, T67(E10)R / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 294 K / pH: 8.7
Details: CO-saturated, 2.8M ammonium sulphate, 100mM Tris-Cl, 1 mM dithionite, crsystal grown in seeded batch, pH 8.7, temperature 294K
Crystal grow
*PLUS
pH: 9 / Method: batch method
Details: Phillips, G.N., (1990) Proteins Struct. Funct. Genet., 7, 358.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 mg/mlprotein11
22.2-2.6 Mammonium sulfate11
320 mMTris-HCl11

-
Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 18, 2001
RadiationMonochromator: No monochromator / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→25 Å / Num. all: 25942 / Num. obs: 25942 / % possible obs: 80.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 13
Reflection shellResolution: 1.55→1.62 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1765 / Rsym value: 0.173 / % possible all: 37.7
Reflection
*PLUS
Num. measured all: 79853 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 0.377 % / Rmerge(I) obs: 0.082

-
Processing

Software
NameVersionClassification
SPECdata collection
PROW+ CCP4data reduction
CNS1refinement
SPECdata reduction
PROWdata scaling
CCP4data scaling
CNS1phasing
RefinementMethod to determine structure: Rigid body from starting model.
Starting model: pdb id 1MYZ

1myz


Resolution: 1.6→13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1465406.53 / Data cutoff high rms absF: 1465406.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Sulfate 501 is on the 3 fold axis. Atoms S and O1 seat right on the axis and are given an occupancy of 0.33. Atoms O3 and O4 are generated by symmetry from atom O2. Unobserved (disordered) ...Details: Sulfate 501 is on the 3 fold axis. Atoms S and O1 seat right on the axis and are given an occupancy of 0.33. Atoms O3 and O4 are generated by symmetry from atom O2. Unobserved (disordered) atoms were removed from the ATOM list: 44 ASP OD2 62 LYS CE 62 LYS NZ 96 LYS CE 96 LYS NZ 98 LYS CD 98 LYS CE 98 LYS NZ 102 LYS CD 102 LYS CE 102 LYS NZ 140 LYS CD 140 LYS CE 140 LYS NZ 147 LYS CD 147 LYS CE 147 LYS NZ The dark structure (Chain ID A, 0.82 occupancy was not refined here. Only the photo excited structure was refined, with the overall occupancies of the two populations of molecules in the crystal. Stereochemical parameters for the Heme were relaxed to allow heme bending and out of plane displacement of the iron. Parameters for Geometry analysis (rmsd for bond length, bond angles, etc ...) given below correspond to the sum of the two states. The values are slightly worse for only the light excited state.
RfactorNum. reflection% reflectionSelection details
Rfree0.173 1135 4.9 %RANDOM
Rwork0.15 ---
all0.1512 23111 --
obs0.15 23111 80.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.1971 Å2 / ksol: 0.33993 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.77 Å20 Å2
2--0.48 Å20 Å2
3----0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 53 143 1411
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.962
X-RAY DIFFRACTIONc_scangle_it3.992.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.227 153 6 %
Rwork0.217 2408 -
obs-2408 53.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1HEM_RELAX.PARHEM_RELAX.TOP
X-RAY DIFFRACTION2CMO_PATCHED.PARCMO_PATCHED.TOP
X-RAY DIFFRACTION3SUL_FREE_CO.PARSUL_FREE_CO.TOP
Refinement
*PLUS
Rfactor Rfree: 0.174 / Rfactor Rwork: 0.15 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

+
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