[English] 日本語
Yorodumi
- PDB-2fgy: Beta Carbonic Anhydrase from the Carboxysomal Shell of Halothioba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fgy
TitleBeta Carbonic Anhydrase from the Carboxysomal Shell of Halothiobacillus neapolitanus (CsoSCA)
Componentscarboxysome shell polypeptide
KeywordsLYASE / beta class of carbonic anhydrase
Function / homology
Function and homology information


carboxysome / carbon fixation / carbonic anhydrase / carbonate dehydratase activity / metal ion binding
Similarity search - Function
Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain / Carboxysome Shell Carbonic Anhydrase, C-terminal domain / : / : / : / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal ...Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain / Carboxysome Shell Carbonic Anhydrase, C-terminal domain / : / : / : / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, C-terminal / 60s Ribosomal Protein L30; Chain: A; / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Carboxysome shell carbonic anhydrase
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsSawaya, M.R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two.
Authors: Sawaya, M.R. / Cannon, G.C. / Heinhorst, S. / Tanaka, S. / Williams, E.B. / Yeates, T.O. / Kerfeld, C.A.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_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: carboxysome shell polypeptide
B: carboxysome shell polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6986
Polymers121,4362
Non-polymers2624
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-163 kcal/mol
Surface area38570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.738, 77.636, 82.714
Angle α, β, γ (deg.)66.84, 78.82, 79.17
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12A
22B
13A
23B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISGLYAA38 - 8966 - 117
211HISGLYBB38 - 8966 - 117
321ASPASNAA91 - 116119 - 144
421ASPASNBB91 - 116119 - 144
112ILEASNAA118 - 348146 - 376
212ILEASNBB118 - 348146 - 376
113SERALAAA350 - 514378 - 542
213SERALABB350 - 514378 - 542

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly is a dimer. It is contained in the asymmetric unit.

-
Components

#1: Protein carboxysome shell polypeptide


Mass: 60718.145 Da / Num. of mol.: 2 / Mutation: Y92H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Description: Gene name is previously known as CsoS3 / Gene: CsoSCA / Plasmid: pcsoS3ProEx / Production host: Escherichia coli (E. coli)
References: GenBank: 3449369, UniProt: O85042*PLUS, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, pH 7.0, 0.2M magnesium chloride, 10% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2005 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→90 Å / Num. all: 52342 / Num. obs: 52789 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.123 / Χ2: 1.089
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.488 / Num. unique all: 5120 / Χ2: 1.215 / % possible all: 94.7

-
Phasing

PhasingMethod: MIRAS
Phasing MADD res high: 2.2 Å / D res low: 75.38 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 52789
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.25-10046.90.714513
7.77-10.2547.60.883675
6.51-7.7747.70.868862
5.72-6.51550.838999
5.15-5.7255.50.8211085
4.73-5.1554.70.8471231
4.4-4.7356.50.841312
4.13-4.4590.8081416
3.9-4.1358.90.781511
3.71-3.966.30.7621565
3.54-3.7165.50.7391655
3.39-3.5464.80.7531724
3.26-3.3967.30.7291816
3.15-3.2670.80.7041863
3.04-3.1572.60.6731938
2.95-3.0473.30.6931996
2.86-2.9578.50.6372032
2.78-2.8688.40.5942112
2.71-2.7886.90.5742201
2.64-2.7188.70.5872202
2.58-2.6488.90.6112245
2.52-2.58900.5992321
2.47-2.5287.50.582414
2.42-2.4788.50.5322408
2.37-2.4289.20.582484
2.32-2.3790.70.5652527
2.28-2.3290.30.5942547
2.24-2.2890.60.5752545
2.2-2.24880.5442590
Phasing MIR der

R cullis centric: 0 / Der set-ID: 1 / Loc centric: 0 / Power centric: 0 / Reflection centric: 0

IDResolution (Å)R cullis acentricLoc acentricPower acentricReflection acentric
Mercury Chloride3.3-1000.8136.41.1315478
mersalyl3-1000.8328.71.0520545
PIP from isodifou using p3.8-1000.9466.20.5610176
native Zn from anodifou u2.2-10013.8052337
iodide from isodifou usin3.9-1000.9269.80.769374
Phasing MIR der shell

R cullis centric: 0 / Loc centric: 0 / Power centric: 0 / Reflection centric: 0

Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricLoc acentricPower acentricReflection acentric
14.6175.38Mercury Chloride0.4728.52.58161
8.0914.61Mercury Chloride0.627.22.47867
5.598.09Mercury Chloride0.6324.92.272173
4.285.59Mercury Chloride0.7733.31.353982
3.464.28Mercury Chloride0.8841.40.816296
2.913.46Mercury Chloride0.9243.90.621999
2.52.91Mercury Chloride0000
2.22.5Mercury Chloride0000
14.6175.38mersalyl0.5231.52.15160
8.0914.61mersalyl0.6226.92.23872
5.598.09mersalyl0.6521.12.342172
4.285.59mersalyl0.7626.11.453974
3.464.28mersalyl0.86300.896297
2.913.46mersalyl0.9431.40.597070
2.52.91mersalyl0000
2.22.5mersalyl0000
14.6175.38PIP from isodifou using p0.8792.10.8164
8.0914.61PIP from isodifou using p0.8675.10.86866
5.598.09PIP from isodifou using p0.8853.90.912169
4.285.59PIP from isodifou using p0.9665.10.523968
3.464.28PIP from isodifou using p0.9872.70.323009
2.913.46PIP from isodifou using p0000
2.52.91PIP from isodifou using p0000
2.22.5PIP from isodifou using p0000
14.6175.38native Zn from anodifou u17.40148
8.0914.61native Zn from anodifou u17.80799
5.598.09native Zn from anodifou u14.502168
4.285.59native Zn from anodifou u15.203901
3.464.28native Zn from anodifou u14.306296
2.913.46native Zn from anodifou u1309410
2.52.91native Zn from anodifou u13.3012906
2.22.5native Zn from anodifou u13.9016709
14.6175.38iodide from isodifou usin0.9780.90.81156
8.0914.61iodide from isodifou usin0.9775.80.82871
5.598.09iodide from isodifou usin0.9159.80.952173
4.285.59iodide from isodifou usin0.969.70.743977
3.464.28iodide from isodifou usin0.9376.50.632197
2.913.46iodide from isodifou usin0000
2.52.91iodide from isodifou usin0000
2.22.5iodide from isodifou usin0000
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1Mercury Chloride30.806Hg0.9910.01710.666
2Mercury Chloride37.723Hg1.354-0.4451.4670.624
3Mercury Chloride67.399Hg1.319-0.2050.7890.471
4Mercury Chloride59.044Hg1.307-0.6991.2850.493
5mersalyl41.162Hg-0.0050.01400.648
6mersalyl50.634Hg1.3560.5560.4660.554
7mersalyl68.796Hg1.3230.7960.7870.39
8mersalyl68.278Hg1.3040.31.2860.424
9PIP from isodifou using p81.799Pt1.7520.3770.3490.541
10PIP from isodifou using p65.227Pt1.160.2360.3720.652
11PIP from isodifou using p81.364Pt0.775-0.1330.850.621
12PIP from isodifou using p74.223Pt1.449-0.1230.7260.588
13native Zn from anodifou u97.373Zn1.3260.3080.2740
14native Zn from anodifou u114.13Zn0.796-0.290.5030
15native Zn from anodifou u100.96Zn2.067-0.0110.2290
16native Zn from anodifou u105.77Zn1.299-0.2130.7950
17iodide from isodifou usin60.7I1.3440.2470.7210.425
18iodide from isodifou usin47.138I1.0410.270.7020.55
19iodide from isodifou usin44.284I1.319-0.1980.7650.483
20iodide from isodifou usin27.562I1.3260.2740.290.66
21iodide from isodifou usin49.048I1.370.5470.4610.411
22iodide from isodifou usin-7.84I1.0080.0130.9930.817

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
BOSdata collection
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→75.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.909 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2656 5 %RANDOM
Rwork0.169 ---
all0.171 52788 --
obs0.171 52788 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.8 Å20.13 Å2
2---0.4 Å20.8 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.2→75.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7370 0 4 557 7931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217530
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.95110232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1865938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16623.529374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.473151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3261566
X-RAY DIFFRACTIONr_chiral_restr0.1230.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025840
X-RAY DIFFRACTIONr_nbd_refined0.2070.23452
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2512
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.25
X-RAY DIFFRACTIONr_mcbond_it0.9241.54817
X-RAY DIFFRACTIONr_mcangle_it1.47527542
X-RAY DIFFRACTIONr_scbond_it2.48233034
X-RAY DIFFRACTIONr_scangle_it3.9184.52690
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1612TIGHT POSITIONAL0.050.05
1612TIGHT THERMAL0.170.5
21735TIGHT POSITIONAL0.050.05
21735TIGHT THERMAL0.180.5
31306TIGHT POSITIONAL0.040.05
31306TIGHT THERMAL0.180.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 186 -
Rwork0.217 3526 -
obs-3712 93.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.55650.21091.17351.53541.40473.10760.0484-0.1511-0.16160.0165-0.16920.27840.1932-0.39870.1208-0.0825-0.07150.0431-0.01430.00480.009812.608627.884848.0212
20.31680.4259-0.38820.8448-0.39561.5187-0.007-0.091-0.04880.107-0.0041-0.07390.00830.13780.011-0.03590.0462-0.0168-0.02720.0098-0.064835.811445.5462.0024
30.910.1312-0.10020.9274-0.28161.0995-0.01160.04970.0012-0.04170.00550.03740.0634-0.0220.0062-0.05590.0066-0.0006-0.0525-0.0135-0.026625.871338.419439.258
41.0688-1.59920.16813.12450.20220.74030.06060.28610.0846-0.12530.0641-0.20310.04410.1106-0.1247-0.0827-0.00710.07210.0432-0.0204-0.043262.8750.908711.1532
50.6923-0.2627-0.38120.7962-0.3751.06870.03520.15850.1139-0.0344-0.007-0.0186-0.0754-0.0488-0.0282-0.03140.0055-0.0129-0.02920.0435-0.030639.54271.206620.722
61.1264-0.0219-0.09440.6602-0.31670.8491-0.01830.0501-0.0914-0.0230.0039-0.01840.07390.03140.0144-0.05340.00450.0055-0.011-0.0226-0.037949.491247.640124.4244
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA38 - 14466 - 172
22AA151 - 397179 - 425
33AA398 - 514426 - 542
44BB38 - 14466 - 172
55BB151 - 397179 - 425
66BB398 - 514426 - 542

+
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