[English] 日本語
Yorodumi
- PDB-1ovr: CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Mn(II)-DF1-L13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ovr
TitleCRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Mn(II)-DF1-L13
Componentsfour-helix bundle model di-Mn(II)-DF1-L13
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 / UNCONVENTIONAL METHOD USING THE GROUP-SUBGROUP RELATION / Resolution: 2.99 Å
AuthorsDi Costanzo, L. / Geremia, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography.
Authors: Geremia, S. / Di Costanzo, L. / Randaccio, L. / Engel, D.E. / Lombardi, A. / Nastri, F. / DeGrado, W.F.
#1: Journal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2003
Title: Sliding Helix Induced Change of Coordination Geomet Model Di-Mn(II) Protein
Authors: Degrado, W.F. / Di Costanzo, L. / Geremia, S. / Lombardi, A. / Pavone, V. / Randaccio, L.
#2: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Toward the De Novo Design of a Catalytically Active Helix-Bundle: A Substrate Accessible Carboxylate-Br Dinuclear Metal Center
Authors: Di Costanzo, L. / Wade, H. / Geremia, S. / Randaccio, L. / Pavone, V. / Degrado, W.F. / Lombardi, A.
#3: 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.
History
DepositionMar 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 20, 2013Group: Derived calculations
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: four-helix bundle model di-Mn(II)-DF1-L13
B: four-helix bundle model di-Mn(II)-DF1-L13
C: four-helix bundle model di-Mn(II)-DF1-L13
D: four-helix bundle model di-Mn(II)-DF1-L13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7589
Polymers23,4844
Non-polymers2755
Water68538
1
A: four-helix bundle model di-Mn(II)-DF1-L13
hetero molecules

A: four-helix bundle model di-Mn(II)-DF1-L13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8524
Polymers11,7422
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2400 Å2
ΔGint-34 kcal/mol
Surface area6510 Å2
MethodPISA
2
B: four-helix bundle model di-Mn(II)-DF1-L13
hetero molecules

B: four-helix bundle model di-Mn(II)-DF1-L13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8524
Polymers11,7422
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area2400 Å2
ΔGint-36 kcal/mol
Surface area6230 Å2
MethodPISA
3
C: four-helix bundle model di-Mn(II)-DF1-L13
D: four-helix bundle model di-Mn(II)-DF1-L13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9075
Polymers11,7422
Non-polymers1653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-37 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.888, 149.177, 38.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ACE / End label comp-ID: MN / Refine code: 6 / Label seq-ID: 1

Dom-IDAuth asym-IDLabel asym-IDAuth seq-ID
1AA - E0 - 50
2BB - F0 - 51
3CC - G0 - 52
4DD - H0 - 53

-
Components

#1: Protein/peptide
four-helix bundle model di-Mn(II)-DF1-L13 / di-Mn(II)-DF1-L13


Mass: 5870.894 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED.
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.57 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: peg 400, Buffer Tris-HCl, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2001 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: 1.2 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
21.21
ReflectionResolution: 2.99→76.4 Å / Num. obs: 5371 / % possible obs: 98.1 % / Redundancy: 2.2 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 16.5
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 7 / Rsym value: 0.168 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: UNCONVENTIONAL METHOD USING THE GROUP-SUBGROUP RELATION
Resolution: 2.99→15 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.819 / SU B: 26.986 / SU ML: 0.526 / Cross valid method: THROUGHOUT / ESU R Free: 0.543
RfactorNum. reflection% reflectionSelection details
Rfree0.30542 240 4.5 %RANDOM
Rwork0.2258 ---
obs0.22931 5371 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.99→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 5 38 1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221710
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8572.0412288
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9393188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.43915364
X-RAY DIFFRACTIONr_chiral_restr0.1320.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021192
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2970.3793
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.570
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.382
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4081.5972
X-RAY DIFFRACTIONr_mcangle_it2.9821568
X-RAY DIFFRACTIONr_scbond_it5.4413734
X-RAY DIFFRACTIONr_scangle_it9.074.5708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 417 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.665
2Bloose positional0.675
3Cloose positional0.815
4Dloose positional0.935
1Aloose thermal7.4110
2Bloose thermal6.3510
3Cloose thermal7.5610
4Dloose thermal6.9910
LS refinement shellResolution: 3→3.075 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.373 23
Rwork0.258 306

+
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