[English] 日本語
Yorodumi
- PDB-3m4b: A Zn-mediated tetrahedral protein lattice cage -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m4b
TitleA Zn-mediated tetrahedral protein lattice cage
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / Four-helix bundle / Heme / Metal-binding / Transport
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsTezcan, F.A. / Ni, T.W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Structural characterization of a microperoxidase inside a metal-directed protein cage.
Authors: Ni, T.W. / Tezcan, F.A.
History
DepositionMar 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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_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.pdbx_leaving_atom_flag / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,06724
Polymers46,5804
Non-polymers3,48720
Water1,45981
1
A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,20272
Polymers139,74112
Non-polymers10,46160
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area37260 Å2
ΔGint-1480 kcal/mol
Surface area53610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.363, 125.363, 164.509
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-110-

ZN

21D-109-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 151
2114D1 - 151

-
Components

#1: Protein
Soluble cytochrome b562 / Cytochrome b-562


Mass: 11645.060 Da / Num. of mol.: 4
Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, I67C, V69I, D73H, D74A, K77H, R98C, Y101C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 1500, 0.1 M Bis-Tris, 0.2 M CaCl2 and 5 mM ZnCl2., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.18 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2009
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.5→90.614 Å / Num. all: 17431 / Num. obs: 17431 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.5 / Num. measured all: 13465 / Num. unique all: 2495 / Rsym value: 0.481 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
MOLREPphasing
RefinementResolution: 2.5→41.27 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.903 / SU B: 21.485 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.725 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25558 1257 7.2 %RANDOM
Rwork0.19791 ---
obs0.20206 16174 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å20 Å2
2---0.21 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 200 81 3537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223629
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3012.0854958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7425439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.97526.529170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65515588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.206158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022822
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21637
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2830.22443
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0790.28
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5211.52211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88923424
X-RAY DIFFRACTIONr_scbond_it1.54631634
X-RAY DIFFRACTIONr_scangle_it2.3794.51516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 823 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.320.5
medium thermal0.772
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 97 -
Rwork0.29 1167 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.7046 Å / Origin y: -12.9889 Å / Origin z: -39.2848 Å
111213212223313233
T-0.0031 Å2-0.0129 Å2-0.0069 Å2--0.0018 Å2-0.0004 Å2---0.0043 Å2
L0.174 °2-0.0208 °2-0.0155 °2-0.1361 °20.0402 °2--0.0124 °2
S-0.0022 Å °-0.075 Å °-0.0524 Å °0.0565 Å °-0.0174 Å °-0.0294 Å °0.0686 Å °0.004 Å °0.0196 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 151
2X-RAY DIFFRACTION1B1 - 151
3X-RAY DIFFRACTION1C1 - 151
4X-RAY DIFFRACTION1D1 - 151
5X-RAY DIFFRACTION1A1 - 139
6X-RAY DIFFRACTION1A - D1 - 109

+
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