[English] 日本語
Yorodumi
- PDB-3mwo: Human carbonic anhydrase II in a doubled monoclinic cell: a re-de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mwo
TitleHuman carbonic anhydrase II in a doubled monoclinic cell: a re-determination
ComponentsCarbonic anhydrase 2
KeywordsLYASE / DOUBLED UNIT CELL / pseudosymmetry / Translational NCS
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsRobbins, A.H. / McKenna, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinic P2(1) with a doubled a axis.
Authors: Robbins, A.H. / Domsic, J.F. / Agbandje-McKenna, M. / McKenna, R.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJun 9, 2010ID: 3KS1
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Apr 20, 2016Group: Refinement description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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_label_asym_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.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_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: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7094
Polymers58,5782
Non-polymers1312
Water13,421745
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3542
Polymers29,2891
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3542
Polymers29,2891
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.981, 41.057, 73.586
Angle α, β, γ (deg.)90.000, 109.330, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Carbonic anhydrase 2 / Carbonic anhydrase II / CA-II / Carbonate dehydratase II / Carbonic anhydrase C / CAC


Mass: 29289.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2, HCA2 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING FOLLOWS THAT REPORTED FOR THE HUMAN CARBONIC ANHYDRASE ISOFORM II, PDB CODE 1CA2.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Tris, 1.2 M sodium citrate, 5 ul + 5 ul droplet, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9782 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2009 / Details: mirrors
RadiationMonochromator: ASYMMETRIC CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 90618 / Num. obs: 90618 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Χ2: 1.083 / Net I/σ(I): 15.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.2 / Num. unique all: 8883 / Rsym value: 0.194 / Χ2: 1.081 / % possible all: 95.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_348refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementStarting model: 3KS1

3ks1
PDB Unreleased entry


Resolution: 1.4→18.279 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.6 / σ(I): 0 / Stereochemistry target values: ML
Details: 3KS1, chain B (altloc B removed), model translated x'=x-1/4 and re-refined
RfactorNum. reflection% reflectionSelection details
Rfree0.184 4581 5.08 %RANDOM
Rwork0.166 ---
all0.167 90110 --
obs0.167 90110 96.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.7 Å2 / ksol: 0.475 e/Å3
Displacement parametersBiso max: 72.97 Å2 / Biso mean: 16.011 Å2 / Biso min: 3.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.507 Å2-0 Å2-0.002 Å2
2---0.477 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.4→18.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 2 745 4845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094343
X-RAY DIFFRACTIONf_angle_d1.2575925
X-RAY DIFFRACTIONf_chiral_restr0.076622
X-RAY DIFFRACTIONf_plane_restr0.007771
X-RAY DIFFRACTIONf_dihedral_angle_d11.981623
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4160.2431510.1982710286192
1.416-1.4330.2161500.1912800295096
1.433-1.450.1891400.1842826296695
1.45-1.4680.2121460.1832821296796
1.468-1.4880.1961770.1752773295096
1.488-1.5080.1981490.1752837298696
1.508-1.530.2041640.1842835299996
1.53-1.5520.211500.172811296196
1.552-1.5770.2051450.1642850299596
1.577-1.6020.1841450.1592830297597
1.602-1.630.1871520.1622877302997
1.63-1.660.2021210.1622859298097
1.66-1.6920.2221640.1632836300097
1.692-1.7260.1781550.1582899305497
1.726-1.7640.1731470.1562846299397
1.764-1.8050.2151530.1572858301197
1.805-1.850.1721710.1552839301097
1.85-1.90.1531610.1562897305897
1.9-1.9560.1651480.1512905305397
1.956-2.0190.1781520.1542862301498
2.019-2.0910.1561640.1492886305098
2.091-2.1740.1751440.1472924306897
2.174-2.2730.1891470.152899304697
2.273-2.3920.1721520.1462910306298
2.392-2.5420.1721560.1592910306698
2.542-2.7380.1851700.1642911308198
2.738-3.0120.1781720.1642883305598
3.012-3.4450.1761330.162959309298
3.445-4.3310.1731610.1552845300695
4.331-18.2810.1741410.2192631277285
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)
10.5207-0.01620.00120.4946-0.1280.6131-0.012-0.0325-0.0102-0.07790.01040.01820.0395-0.01240.00270.039-0.00450.00050.03190.00040.03259.4951.38515.831
20.6026-0.083-0.06960.46350.00930.4402-0.0117-0.04810.0032-0.0010.0199-0.02270.0132-0.0053-0.00860.0356-0.0007-0.00330.0355-0.00410.042751.6291.39515.713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 263:781 ) OR ( CHAIN B AND RESID 126:780 )A263 - 781
2X-RAY DIFFRACTION1( CHAIN A AND RESID 263:781 ) OR ( CHAIN B AND RESID 126:780 )B126 - 780
3X-RAY DIFFRACTION2( CHAIN B AND RESID 4:125 )B4 - 125

+
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