[English] 日本語
Yorodumi
- PDB-4yf4: Crystal structure of Rv1284 in the presence of polycarpine at mil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yf4
TitleCrystal structure of Rv1284 in the presence of polycarpine at mildly acidic pH
ComponentsBeta-carbonic anhydrase 1
KeywordsLYASE / beta-carbonic anhydrase
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-carbonic anhydrase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHofmann, A.
CitationJournal: Febs J. / Year: 2015
Title: Chemical probing suggests redox-regulation of the carbonic anhydrase activity of mycobacterial Rv1284.
Authors: Nienaber, L. / Cave-Freeman, E. / Cross, M. / Mason, L. / Bailey, U.M. / Amani, P. / A Davis, R. / Taylor, P. / Hofmann, A.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-carbonic anhydrase 1
B: Beta-carbonic anhydrase 1
C: Beta-carbonic anhydrase 1
D: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,45314
Polymers77,0234
Non-polymers43010
Water5,783321
1
A: Beta-carbonic anhydrase 1
B: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7277
Polymers38,5122
Non-polymers2155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-146 kcal/mol
Surface area13020 Å2
MethodPISA
2
C: Beta-carbonic anhydrase 1
D: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7277
Polymers38,5122
Non-polymers2155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-147 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.142, 154.345, 157.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21A-327-

HOH

31C-315-

HOH

41C-321-

HOH

-
Components

#1: Protein
Beta-carbonic anhydrase 1 / Beta-CA 1 / Carbonate dehydratase 1 / mtCA 1


Mass: 19255.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: mtcA1, canA, MT1322 / Plasmid: pCR T7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21AI / References: UniProt: P9WPJ6, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1 M K/Na tartrate, 0.1 M MES/NaOH, 10 mM polycarpine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95382 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95382 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 105432 / % possible obs: 98.8 % / Redundancy: 5.4 % / Rsym value: 0.06 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.7 / % possible all: 92.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLK

1ylk


Resolution: 1.8→24.88 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 5336 5.06 %
Rwork0.194 --
obs0.196 105432 95.4 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.12 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0604 Å20 Å20 Å2
2---4.6771 Å20 Å2
3---4.7374 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 10 321 5415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085218
X-RAY DIFFRACTIONf_angle_d1.0967096
X-RAY DIFFRACTIONf_dihedral_angle_d12.561946
X-RAY DIFFRACTIONf_chiral_restr0.073824
X-RAY DIFFRACTIONf_plane_restr0.005927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8002-1.82070.32411400.30452322X-RAY DIFFRACTION68
1.8207-1.84210.33411390.29992651X-RAY DIFFRACTION74
1.8421-1.86450.36181280.29382734X-RAY DIFFRACTION79
1.8645-1.88810.3051300.29792960X-RAY DIFFRACTION84
1.8881-1.9130.41271780.33632947X-RAY DIFFRACTION85
1.913-1.93920.47611560.34693114X-RAY DIFFRACTION89
1.9392-1.96680.26351780.22543333X-RAY DIFFRACTION94
1.9668-1.99620.2391750.22023377X-RAY DIFFRACTION97
1.9962-2.02740.26821820.20643464X-RAY DIFFRACTION99
2.0274-2.06060.26181930.20083471X-RAY DIFFRACTION100
2.0606-2.09610.2461750.1893559X-RAY DIFFRACTION100
2.0961-2.13420.24562280.18623423X-RAY DIFFRACTION100
2.1342-2.17520.24191970.18573515X-RAY DIFFRACTION100
2.1752-2.21960.20531840.1923473X-RAY DIFFRACTION100
2.2196-2.26780.40581900.30393308X-RAY DIFFRACTION95
2.2678-2.32060.22631820.18293452X-RAY DIFFRACTION99
2.3206-2.37850.29441800.1793528X-RAY DIFFRACTION100
2.3785-2.44280.23052060.17473467X-RAY DIFFRACTION100
2.4428-2.51460.20871720.17733505X-RAY DIFFRACTION100
2.5146-2.59570.23331920.18793467X-RAY DIFFRACTION100
2.5957-2.68840.26071950.19343527X-RAY DIFFRACTION100
2.6884-2.79590.25491910.19053480X-RAY DIFFRACTION100
2.7959-2.92290.25771890.19433507X-RAY DIFFRACTION100
2.9229-3.07680.25551650.18893486X-RAY DIFFRACTION100
3.0768-3.26910.24061780.1883543X-RAY DIFFRACTION100
3.2691-3.52090.23621930.17723464X-RAY DIFFRACTION100
3.5209-3.8740.21851770.17573511X-RAY DIFFRACTION100
3.874-4.43190.19891590.14883525X-RAY DIFFRACTION100
4.4319-5.57330.16341890.15583489X-RAY DIFFRACTION100
5.5733-24.88680.19661950.18963494X-RAY DIFFRACTION99
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)
10.8058-0.01610.20981.5225-0.2481.12450.02830.06870.0001-0.0871-0.06070.06140.01020.01920.02850.1191-0.00040.00190.1222-0.01470.104-0.1603-36.5332-17.1411
20.86870.0153-0.33011.54760.04411.3982-0.0241-0.0746-0.03380.1106-0.12120.08590.0030.01770.12980.11-0.0046-0.0040.13140.00380.1304-27.77940.0384-22.5067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A OR CHAIN B
2X-RAY DIFFRACTION2CHAIN C OR CHAIN D

+
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