[English] 日本語
Yorodumi
- PDB-1dmy: COMPLEX BETWEEN MURINE MITOCHONDRIAL CARBONIC ANYHDRASE V AND THE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dmy
TitleCOMPLEX BETWEEN MURINE MITOCHONDRIAL CARBONIC ANYHDRASE V AND THE TRANSITION STATE ANALOGUE ACETAZOLAMIDE
ComponentsMURINE CARBONIC ANHYDRASE V
KeywordsLYASE (OXO-ACID) / PROTON TRANSFER
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / gluconeogenesis / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / mitochondrion / zinc ion binding / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase 5A, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsBoriack-Sjodin, P.A. / Christianson, D.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Structure determination of murine mitochondrial carbonic anhydrase V at 2.45-A resolution: implications for catalytic proton transfer and inhibitor design.
Authors: Boriack-Sjodin, P.A. / Heck, R.W. / Laipis, P.J. / Silverman, D.N. / Christianson, D.W.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Catalytic Properties of Mouse Carbonic Anhydrase V
Authors: Heck, R.W. / Tanhauser, S.M. / Manda, R. / TU, C. / Laipis, P.J. / Silverman, D.N.
History
DepositionOct 4, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.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_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: MURINE CARBONIC ANHYDRASE V
B: MURINE CARBONIC ANHYDRASE V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1276
Polymers56,5522
Non-polymers5754
Water1,802100
1
A: MURINE CARBONIC ANHYDRASE V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5643
Polymers28,2761
Non-polymers2882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MURINE CARBONIC ANHYDRASE V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5643
Polymers28,2761
Non-polymers2882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.690, 60.370, 60.440
Angle α, β, γ (deg.)67.65, 75.26, 75.21
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 30 / 2: CIS PROLINE - PRO A 202 / 3: CIS PROLINE - PRO B 30 / 4: CIS PROLINE - PRO B 202
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999912, 0.003781, -0.01269), (0.010869, -0.313023, -0.949683), (-0.007563, -0.949738, 0.312954)
Vector: 116.35023, 108.07323, 37.70745)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 25 .. A 261 B 25 .. B 261 0.445

-
Components

#1: Protein MURINE CARBONIC ANHYDRASE V / CARBONATE DEHYDROGENASE / MCAVC


Mass: 28275.854 Da / Num. of mol.: 2
Mutation: TRUNCATION OF MITOCHONDRIAL LEADER SEQUENCE AND FIRST 21 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/CJ
Description: TRUNCATED VERSION OF PROTEIN WITH 21 N TERMINAL RESIDUES REMOVED (SEE HECK ET AL., JBC, VOL 269 (1994) PP 24742-24746)
Cell line: BL21 / Gene: MCA5C / Organ: LIVER / Organelle: MITOCHONDRIA / Plasmid: PET31 T7 / Gene (production host): MCA5C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P23589, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
Common name: PEG8000

-
Data collection

DiffractionAmbient temp details: ROOM
Diffraction sourceWavelength: 1.5418
DetectorType: R-AXIS IIC / Detector: IMAGE PLATE AREA DETECTOR / Date: Dec 19, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→19.9 Å / Num. obs: 21645 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.073
Reflection
*PLUS
Rmerge(I) obs: 0.073

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MOSFLMdata reduction
RefinementResolution: 2.45→8 Å / σ(F): 2
Details: CRYST1 TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA: TWO MOLECULES IN UNIT CELL RELATED BY NONCRYSTALLOGRAPHIC SYMMETRY SYMMETRY OPERATIONS FOR NON-STANDARD SETTING:
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 17382 79 %
Refinement stepCycle: LAST / Resolution: 2.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 28 100 3938
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.05
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.348
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.05
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.348

+
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