[English] 日本語
Yorodumi
- PDB-2rcf: Carboxysome Shell protein, OrfA from H. Neapolitanus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rcf
TitleCarboxysome Shell protein, OrfA from H. Neapolitanus
ComponentsUnidentified carboxysome polypeptide
KeywordsSTRUCTURAL PROTEIN / cyclic pentamer
Function / homology
Function and homology information


carboxysome / carbon fixation
Similarity search - Function
EutN/Ccml / Carboxysome shell vertex protein CsoS4A / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Carboxysome shell vertex protein CsoS4A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsKerfeld, C.A. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Science / Year: 2008
Title: Atomic-level models of the bacterial carboxysome shell.
Authors: Tanaka, S. / Kerfeld, C.A. / Sawaya, M.R. / Cai, F. / Heinhorst, S. / Cannon, G.C. / Yeates, T.O.
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Unidentified carboxysome polypeptide
B: Unidentified carboxysome polypeptide
C: Unidentified carboxysome polypeptide
D: Unidentified carboxysome polypeptide
E: Unidentified carboxysome polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1699
Polymers49,8575
Non-polymers3124
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.933, 86.780, 35.214
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61A
71B
81C
91D
101E

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSER4AA32 - 5532 - 55
21GLYGLYSERSER4BB32 - 5532 - 55
31GLYGLYSERSER4CC32 - 5532 - 55
41GLYGLYSERSER4DD32 - 5532 - 55
51GLYGLYSERSER4EE32 - 5532 - 55
62SERSERILEILE5AA56 - 7756 - 77
72SERSERILEILE5BB56 - 7756 - 77
82SERSERILEILE5CC56 - 7756 - 77
92SERSERILEILE5DD56 - 7756 - 77
102SERSERILEILE5EE56 - 7756 - 77

-
Components

#1: Protein
Unidentified carboxysome polypeptide


Mass: 9971.439 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: ORFA / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O85043
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8.0, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→90 Å / Num. obs: 20056 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.175 / Χ2: 1.057 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.236.70.50720041.09199
2.23-2.3270.43419661.08199.6
2.32-2.427.20.39819831.059199.6
2.42-2.557.30.35820101.021199.7
2.55-2.717.30.28820151.098199.7
2.71-2.927.40.2219991.031199.8
2.92-3.217.30.16420141.09199.8
3.21-3.687.30.12819771.135199.9
3.68-4.637.10.10620181.0041100
4.63-907.10.10120700.9661100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRYSTAL STRUCTURE OF CCML PDB ID 2QW7

2qw7


Resolution: 2.15→43.4 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.751 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1022 5.1 %RANDOM
Rwork0.184 ---
obs0.187 20042 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.02 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 19 267 3301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223088
X-RAY DIFFRACTIONr_bond_other_d0.0010.022081
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.9674192
X-RAY DIFFRACTIONr_angle_other_deg0.77735132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6775399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5924.653101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70815530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4791515
X-RAY DIFFRACTIONr_chiral_restr0.0540.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_nbd_refined0.2040.2528
X-RAY DIFFRACTIONr_nbd_other0.1860.22218
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21443
X-RAY DIFFRACTIONr_nbtor_other0.0820.21654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.223
X-RAY DIFFRACTIONr_mcbond_it1.28222155
X-RAY DIFFRACTIONr_mcbond_other0.2492814
X-RAY DIFFRACTIONr_mcangle_it1.79533237
X-RAY DIFFRACTIONr_scbond_it1.16821221
X-RAY DIFFRACTIONr_scangle_it1.6523955
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A402MEDIUM POSITIONAL0.120.5
2B402MEDIUM POSITIONAL0.10.5
3C402MEDIUM POSITIONAL0.120.5
4D402MEDIUM POSITIONAL0.20.5
5E402MEDIUM POSITIONAL0.140.5
1A132LOOSE POSITIONAL0.445
2B132LOOSE POSITIONAL0.575
3C132LOOSE POSITIONAL0.375
4D132LOOSE POSITIONAL0.425
5E132LOOSE POSITIONAL0.345
1A402MEDIUM THERMAL0.422
2B402MEDIUM THERMAL0.322
3C402MEDIUM THERMAL0.342
4D402MEDIUM THERMAL0.312
5E402MEDIUM THERMAL0.382
1A132LOOSE THERMAL2.7410
2B132LOOSE THERMAL1.110
3C132LOOSE THERMAL0.9410
4D132LOOSE THERMAL0.9910
5E132LOOSE THERMAL1.410
LS refinement shellResolution: 2.155→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 73 -
Rwork0.209 1322 -
all-1395 -
obs--93.44 %
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)
11.7697-0.4401-0.53963.26590.81771.98040.0554-0.0643-0.0293-0.0746-0.0745-0.12610.00010.08360.0191-0.0680.0042-0.0154-0.03680.0022-0.0145-0.5635-13.4671-5.9275
23.00590.18680.46191.12330.63711.8983-0.03090.0051-0.1201-0.02020.0171-0.01240.1163-0.09120.0138-0.0292-0.0201-0.0044-0.08080.0195-0.0471-17.2907-22.2867-5.3833
30.9213-0.51150.1162.4915-0.17281.81-0.02930.0252-0.0053-0.05380.02870.186-0.1016-0.21580.0006-0.071-0.02360.00220.00090.0161-0.0196-31.8576-9.229-5.411
41.41090.7279-0.04382.151-0.83662.1718-0.0008-0.00150.0841-0.03130.00880.0888-0.0408-0.1192-0.008-0.02750.04670.0111-0.0494-0.0201-0.0438-24.51368.3403-4.9872
52.5844-0.2643-1.04721.01020.69972.349-0.01490.0194-0.0119-0.05630.0255-0.0519-0.05260.1553-0.0106-0.031-0.0347-0.0171-0.0583-0.0137-0.0333-4.70147.0592-5.3644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 821 - 82
2X-RAY DIFFRACTION2BB1 - 811 - 81
3X-RAY DIFFRACTION3CC1 - 811 - 81
4X-RAY DIFFRACTION4DD1 - 801 - 80
5X-RAY DIFFRACTION5EE1 - 801 - 80

+
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