[English] 日本語
Yorodumi
- PDB-3qv0: Crystal structure of Saccharomyces cerevisiae Mam33 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qv0
TitleCrystal structure of Saccharomyces cerevisiae Mam33
ComponentsMitochondrial acidic protein MAM33
KeywordsPROTEIN BINDING / a bowl like structure / mitochondrial oxidative phosphorylation
Function / homology
Function and homology information


RHOC GTPase cycle / mitochondrial ribosome binding / RHOA GTPase cycle / mitochondrial ribosome assembly / aerobic respiration / cytosolic ribosome assembly / mitochondrial matrix / mitochondrion
Similarity search - Function
Mitochondrial Matrix Protein; Chain A / Mitochondrial glycoprotein / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Roll / Alpha Beta
Similarity search - Domain/homology
Mitochondrial acidic protein MAM33
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJiang, Y.L. / Pu, Y.G. / Ma, X.X. / Chen, Y. / Zhou, C.Z.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structures and putative interface of Saccharomyces cerevisiae mitochondrial matrix proteins Mmf1 and Mam33.
Authors: Pu, Y.G. / Jiang, Y.L. / Ye, X.D. / Ma, X.X. / Guo, P.C. / Lian, F.M. / Teng, Y.B. / Chen, Y. / Zhou, C.Z.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitochondrial acidic protein MAM33


Theoretical massNumber of molelcules
Total (without water)25,8751
Polymers25,8751
Non-polymers00
Water1,56787
1
A: Mitochondrial acidic protein MAM33

A: Mitochondrial acidic protein MAM33

A: Mitochondrial acidic protein MAM33


Theoretical massNumber of molelcules
Total (without water)77,6253
Polymers77,6253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6950 Å2
ΔGint-53 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.755, 118.755, 118.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein Mitochondrial acidic protein MAM33


Mass: 25875.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAM33, YIL070C / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40513
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 20% Polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9194 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.1→83.97 Å / Num. obs: 16404 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 37.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 21.3 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 10.3 / Num. unique all: 1605 / Rsym value: 0.393 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P32

1p32


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.361 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25219 830 5.1 %RANDOM
Rwork0.22741 ---
obs0.22866 15573 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.453 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 0 87 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221469
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9571983
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0775175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74825.69679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90715254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.174155
X-RAY DIFFRACTIONr_chiral_restr0.0710.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211128
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6191.5892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1921437
X-RAY DIFFRACTIONr_scbond_it1.7753577
X-RAY DIFFRACTIONr_scangle_it2.9664.5546
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 63 -
Rwork0.207 1149 -
obs--100 %
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)
12.3659-0.0218-0.87590.794-0.48571.540.02180.1013-0.0442-0.26390.01770.10030.0637-0.2388-0.03950.20540.0226-0.0490.1232-0.00630.1063-5.51818.383-5.377
20.53970.3329-0.63140.6484-0.84311.9394-0.00760.113-0.1006-0.1850.03170.0650.0527-0.1939-0.02410.20240.0571-0.01890.1709-0.01610.1633-5.23118.172-4.229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 266
2X-RAY DIFFRACTION2A301 - 387

+
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