[English] 日本語
Yorodumi
- PDB-2ev4: Structure of Rv1264N, the regulatory domain of the mycobacterial ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ev4
TitleStructure of Rv1264N, the regulatory domain of the mycobacterial adenylyl cylcase Rv1264, with a salt precipitant
ComponentsHypothetical protein Rv1264/MT1302
KeywordsLYASE / Alpha-helical / Regulatory Domain of Adenylyl cyclase / oleic acid
Function / homology
Function and homology information


adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / response to pH / adenylate cyclase inhibitor activity / manganese ion binding / intracellular signal transduction / lipid binding / protein homodimerization activity / ATP binding
Similarity search - Function
Adenylate cyclase regulatory domain / Adenylate cyclase regulatory domain / : / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
OLEIC ACID / pH-sensitive adenylate cyclase Rv1264 / pH-sensitive adenylate cyclase Rv1264
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsFindeisen, F. / Tews, I. / Sinning, I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The structure of the regulatory domain of the adenylyl cyclase Rv1264 from Mycobacterium tuberculosis with bound oleic acid
Authors: Findeisen, F. / Linder, J.U. / Schultz, A. / Schultz, J.E. / Brugger, B. / Wieland, F. / Sinning, I. / Tews, I.
History
DepositionOct 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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 / _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: Hypothetical protein Rv1264/MT1302
B: Hypothetical protein Rv1264/MT1302
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9395
Polymers48,3392
Non-polymers6003
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-74 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.081, 53.916, 89.814
Angle α, β, γ (deg.)90.00, 132.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1004-

HOH

21A-1005-

HOH

31B-212-

HOH

-
Components

#1: Protein Hypothetical protein Rv1264/MT1302 / ADENYLYL CYCLASE


Mass: 24169.354 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1264 / Plasmid: pQE 30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q11055, UniProt: P9WMU9*PLUS, adenylate cyclase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulphate, TRIS, lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 11, 2003
RadiationMonochromator: Khozu monochromator with a McLennon controller containing a LN2 cooled Si111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. all: 19629 / Num. obs: 18893 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.1
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1948 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.936 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26616 961 5.1 %RANDOM
Rwork0.21818 ---
all0.22069 19569 --
obs0.22069 17868 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.303 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å2-1.05 Å2
2--0.6 Å20 Å2
3----0.49 Å2
Refine analyzeLuzzati coordinate error obs: 0.437 Å
Refinement stepCycle: LAST / Resolution: 2.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 41 111 2969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222921
X-RAY DIFFRACTIONr_bond_other_d0.0020.022872
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9963948
X-RAY DIFFRACTIONr_angle_other_deg0.92636625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8155367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71423.684133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96115512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2531532
X-RAY DIFFRACTIONr_chiral_restr0.0730.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
X-RAY DIFFRACTIONr_nbd_refined0.2110.2699
X-RAY DIFFRACTIONr_nbd_other0.1980.23039
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21394
X-RAY DIFFRACTIONr_nbtor_other0.0830.21733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3570.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4050.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5740.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9721.52390
X-RAY DIFFRACTIONr_mcbond_other0.1581.5754
X-RAY DIFFRACTIONr_mcangle_it1.12422949
X-RAY DIFFRACTIONr_scbond_it2.03531169
X-RAY DIFFRACTIONr_scangle_it3.0284.5999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 77 -
Rwork0.289 1290 -
obs-1446 94.54 %
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)
115.7694-4.69563.507615.0756-1.04312.66780.35080.0715-0.6309-0.2572-0.52060.26610.6463-1.44240.1698-0.24920.02450.03790.0451-0.0537-0.0351-26.6541-15.6695-14.0838
21.6449-0.49210.92194.8686-0.25744.61020.113-0.0455-0.3146-0.4445-0.23690.70420.7348-0.82430.1239-0.2082-0.16860.0243-0.0114-0.0521-0.0327-14.828-36.621.8379
37.4958-4.60847.86576.9846-6.773312.0181-0.2834-0.55280.2360.60650.51090.5785-0.7717-0.8437-0.2275-0.3007-0.00710.0928-0.2249-0.02-0.1703-9.4658-16.75384.2349
42.5502-0.46051.309410.73750.693221.3988-0.11280.42810.3454-0.785-0.2179-0.6157-1.60711.98130.3308-0.0099-0.09370.00190.18150.0871-0.107213.4449-38.407832.0635
52.9479-0.27321.26496.89780.90812.88720.0535-0.38670.18290.38430.0501-0.1802-0.1391-0.0099-0.1037-0.1934-0.01920.0228-0.1756-0.0833-0.285-1.4951-17.154517.4316
65.3839-5.46946.81677.5745-7.197711.33760.2175-0.3579-0.5877-0.01210.25120.57080.6309-0.147-0.4686-0.1954-0.07810.0513-0.2261-0.0063-0.2139-3.0245-37.726113.3022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 5623 - 68
2X-RAY DIFFRACTION2AA57 - 14969 - 161
3X-RAY DIFFRACTION3AA150 - 196162 - 208
4X-RAY DIFFRACTION4BB12 - 5624 - 68
5X-RAY DIFFRACTION5BB57 - 14969 - 161
6X-RAY DIFFRACTION6BB150 - 194162 - 206

+
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