[English] 日本語
Yorodumi
- PDB-5lla: Crystal structure of human carbonic anhydrase isozyme XIII with 4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lla
TitleCrystal structure of human carbonic anhydrase isozyme XIII with 4-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide
ComponentsCarbonic anhydrase 13
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / cytosol / 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
Chem-6YQ / CITRIC ACID / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Chemistryselect / Year: 2017
Title: Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases
Authors: Capkauskaite, E. / Linkuviene, V. / Smirnov, A. / Milinaviciute, G. / Timm, D. / Kasiliauskaite, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionJul 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Jan 10, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Carbonic anhydrase 13
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56510
Polymers59,2272
Non-polymers1,3398
Water9,908550
1
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2835
Polymers29,6131
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2835
Polymers29,6131
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.023, 57.276, 159.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Carbonic anhydrase 13 / Carbonate dehydratase XIII / Carbonic anhydrase XIII / CA-XIII


Mass: 29613.318 Da / Num. of mol.: 2 / Fragment: human carbonic anhydrase XIII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N1Q1, carbonic anhydrase

-
Non-polymers , 5 types, 558 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6YQ / 4-[2-(benzimidazol-1-yl)ethanoyl]-2-chloranyl-benzenesulfonamide


Mass: 349.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12ClN3O3S
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.16 Å3/Da / Density % sol: 42.99 % / Mosaicity: 0.17 °
Crystal growTemperature: 291 K / Method: evaporation
Details: Crystallization buffer: 0.1M ammonium citrate (pH 7), 0.1M sodium acetate (pH 4.5) and 26% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.5→159.284 Å / Num. all: 82297 / Num. obs: 82297 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rpim(I) all: 0.016 / Rrim(I) all: 0.04 / Rsym value: 0.033 / Net I/av σ(I): 15.123 / Net I/σ(I): 26.8 / Num. measured all: 524723
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.586.60.3582.2199.2
1.58-1.686.40.2493199.4
1.68-1.796.40.1514.9199.3
1.79-1.946.60.0848.9199.8
1.94-2.126.20.05114.5199.2
2.12-2.376.60.03719.6199.7
2.37-2.746.10.02923.8199.4
2.74-3.356.40.02327.2199.1
3.35-4.745.90.01931.5198.5
4.74-159.2845.80.01732.7198.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KNN

4knn


Resolution: 1.5→79.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 8196 10 %RANDOM
Rwork0.1787 ---
obs0.1821 74022 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 82.81 Å2 / Biso mean: 20.079 Å2 / Biso min: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 1.5→79.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 82 550 4740
Biso mean--41.03 28.89 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.024440
X-RAY DIFFRACTIONr_angle_refined_deg2.4521.9626067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96724.039203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70615705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3431522
X-RAY DIFFRACTIONr_chiral_restr0.2330.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213490
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 591 -
Rwork0.352 5398 -
all-5989 -
obs--98.99 %

+
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://pdbjlc1.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