[English] 日本語
Yorodumi
- PDB-1jmb: CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jmb
TitleCRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL
ComponentsPROTEIN (FOUR-HELIX BUNDLE MODEL)
KeywordsDE NOVO PROTEIN / ALPHA-HELICAL BUNDLE / PROTEIN DESIGN
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / :
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDi Costanzo, L. / Geremia, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2001
Title: Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center.
Authors: Di Costanzo, L. / Wade, H. / Geremia, S. / Randaccio, L. / Pavone, V. / DeGrado, W.F. / Lombardi, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Retrostructural Analysis of Metalloproteins: Application to the Design of a Minimal Model for Diiron Proteins
Authors: Lombardi, A. / Summa, C.M. / Geremia, S. / Randaccio, L. / Pavone, V. / DeGrado, W.F.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1999
Title: Tertiary Templates for the Design of Diiron Proteins
Authors: Summa, C.M. / Lombardi, A. / Lewis, M. / DeGrado, W.F.
#3: Journal: Annu.Rev.Biochem. / Year: 1999
Title: De Novo Design and Structural Characterization of Proteins and Metalloproteins
Authors: DeGrado, W.F. / Summa, C.M. / Pavone, V. / Nastri, F. / Lombardi, A.
History
DepositionJul 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (FOUR-HELIX BUNDLE MODEL)
B: PROTEIN (FOUR-HELIX BUNDLE MODEL)
C: PROTEIN (FOUR-HELIX BUNDLE MODEL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8088
Polymers17,4863
Non-polymers3215
Water55831
1
A: PROTEIN (FOUR-HELIX BUNDLE MODEL)
hetero molecules

A: PROTEIN (FOUR-HELIX BUNDLE MODEL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9246
Polymers11,6582
Non-polymers2664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: PROTEIN (FOUR-HELIX BUNDLE MODEL)
C: PROTEIN (FOUR-HELIX BUNDLE MODEL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8465
Polymers11,6582
Non-polymers1883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-28 kcal/mol
Surface area5900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.121, 112.451, 79.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein/peptide PROTEIN (FOUR-HELIX BUNDLE MODEL)


Mass: 5828.813 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 200, DMSO, Mn(CH3COO)2 , TRIS, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mg/mlprotein1drop
30.03 M1reservoirMn(CH3COO)2
40.1 MTris-HCl1reservoirpH7.5
2PEG2001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2000 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 18643 / Num. obs: 7562 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 5.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.329 / % possible all: 90.5
Reflection
*PLUS
Lowest resolution: 21.2 Å / Num. measured all: 18643
Reflection shell
*PLUS
% possible obs: 90.5 % / Mean I/σ(I) obs: 2.2

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THEORETICAL MODEL

Resolution: 2.2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.318 361 5 %RANDOM
Rwork0.247 ---
obs-18643 87.3 %-
Displacement parametersBiso mean: 41.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 15 31 1285
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0290.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3891.5
X-RAY DIFFRACTIONp_mcangle_it3.9682
X-RAY DIFFRACTIONp_scbond_it6.2053
X-RAY DIFFRACTIONp_scangle_it9.5224.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 7186 / % reflection Rfree: 5 % / Rfactor obs: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.8 Å2
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 4.3

+
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