[English] 日本語
Yorodumi
- PDB-6sc4: Gamma-Carbonic Anhydrase from the Haloarchaeon Halobacterium sp. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sc4
TitleGamma-Carbonic Anhydrase from the Haloarchaeon Halobacterium sp.
ComponentsUncharacterized protein
KeywordsMETAL BINDING PROTEIN / Red Sea Brine Pool Discovery Deep / Halophile / Salt Adaptation / Enzyme Engineering
Function / homology
Function and homology information


: / : / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / Acetyltransferase
Similarity search - Component
Biological speciescandidate division MSBL1 archaeon SCGC-AAA259I09 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVogler, M. / Karan, R. / Renn, D. / Vancea, A. / Vielberg, V.-T. / Groetzinger, S.W. / DasSarma, P. / Das Sarma, S. / Eppinger, J. / Groll, M. / Rueping, M.
CitationJournal: Front Microbiol / Year: 2020
Title: Crystal Structure and Active Site Engineering of a Halophilic gamma-Carbonic Anhydrase.
Authors: Vogler, M. / Karan, R. / Renn, D. / Vancea, A. / Vielberg, M.T. / Grotzinger, S.W. / DasSarma, P. / DasSarma, S. / Eppinger, J. / Groll, M. / Rueping, M.
History
DepositionJul 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 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
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.ptnr1_symmetry / _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.ptnr2_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_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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,02743
Polymers105,8625
Non-polymers3,16538
Water9,368520
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,29624
Polymers63,5173
Non-polymers1,77921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-28 kcal/mol
Surface area20740 Å2
MethodPISA
2
D: Uncharacterized protein
hetero molecules

D: Uncharacterized protein
hetero molecules

D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,94330
Polymers63,5173
Non-polymers2,42627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9880 Å2
ΔGint7 kcal/mol
Surface area20030 Å2
MethodPISA
3
E: Uncharacterized protein
hetero molecules

E: Uncharacterized protein
hetero molecules

E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,24927
Polymers63,5173
Non-polymers1,73224
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
Buried area8930 Å2
ΔGint-14 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)362.640, 362.640, 362.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11D-203-

SO4

21D-203-

SO4

31D-204-

SO4

41D-204-

SO4

51D-207-

TRS

61D-208-

TRS

71D-208-

TRS

81E-902-

SO4

91E-906-

TRS

101E-906-

TRS

111D-1001-

HOH

121D-1002-

HOH

131D-1099-

HOH

141E-1109-

HOH

151E-1111-

HOH

161E-1112-

HOH

171E-1119-

HOH

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Uncharacterized protein


Mass: 21172.318 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) candidate division MSBL1 archaeon SCGC-AAA259I09 (archaea)
Gene: AKJ37_07020 / Production host: Halobacterium sp. (Halophile) / Strain (production host): NRC-1 / Variant (production host): DELTAura3 / References: UniProt: A0A133ULQ3

-
Non-polymers , 7 types, 558 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cd
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.69 Å3/Da / Density % sol: 73.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.05 M CdSO4, 0.8 M NaOAc

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.28 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 62896 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.8
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 12673 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V3W

1v3w


Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.345 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.193
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 3124 5 %RANDOM
Rwork0.1773 ---
obs0.1787 59365 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.68 Å2 / Biso mean: 47.499 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6917 0 91 520 7528
Biso mean--72.85 45.98 -
Num. residues----890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197110
X-RAY DIFFRACTIONr_bond_other_d0.0020.026913
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9619602
X-RAY DIFFRACTIONr_angle_other_deg0.857316079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8725310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.623151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.371540
X-RAY DIFFRACTIONr_chiral_restr0.0680.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021254
LS refinement shellResolution: 2.6→2.666 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 222 -
Rwork0.334 4215 -
all-4437 -
obs--100 %

+
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