[English] 日本語
Yorodumi
- PDB-2hy1: Crystal structure of Rv0805 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hy1
TitleCrystal structure of Rv0805
ComponentsRv0805
KeywordsHYDROLASE / metallophosphoesterase / cAMP / phosphodiesterase / bi-nuclear active site
Function / homology
Function and homology information


2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / : / cell wall modification / 3',5'-cyclic-nucleotide phosphodiesterase / phosphate ion binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / peptidoglycan-based cell wall / ferric iron binding ...2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / : / cell wall modification / 3',5'-cyclic-nucleotide phosphodiesterase / phosphate ion binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / peptidoglycan-based cell wall / ferric iron binding / manganese ion binding / iron ion binding / nucleotide binding / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Cyclic nucleotide phosphodiesterase GpdQ/CpdA-like / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / PHOSPHATE ION / cAMP/cGMP dual specificity phosphodiesterase MT0825 / cAMP/cGMP dual specificity phosphodiesterase Rv0805
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsShenoy, A.R. / Capuder, M. / Draskovic, P. / Lamba, D. / Visweswariah, S.S. / Podobnik, M.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural and Biochemical Analysis of the Rv0805 Cyclic Nucleotide Phosphodiesterase from Mycobacterium tuberculosis.
Authors: Shenoy, A.R. / Capuder, M. / Draskovic, P. / Lamba, D. / Visweswariah, S.S. / Podobnik, M.
#1: Journal: Biochemistry / Year: 2005
Title: The Rv0805 Gene from Mycobacterium tuberculosis Encodes a 3',5'-Cyclic Nucleotide Phosphodiesterase: Biochemical and Mutational Analysis
Authors: Shenoy, A.R. / Sreenath, N. / Podobnik, M. / Kovacevic, M. / Visweswariah, S.S.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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: Rv0805
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1644
Polymers29,9581
Non-polymers2063
Water1,856103
1
A: Rv0805
hetero molecules

A: Rv0805
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3278
Polymers59,9162
Non-polymers4126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)55.263, 94.299, 50.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations:-X,-Y,Z

-
Components

#1: Protein Rv0805 / Icc protein


Mass: 29957.982 Da / Num. of mol.: 1 / Fragment: catalytic core (residues 1-278)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0805 / Plasmid: pProExHTc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O06629, UniProt: P9WP65*PLUS, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, MgCl2, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2006 / Details: monochromator, mirrors
RadiationMonochromator: DOUBLE CRYSTAL (Si) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.93→50.9 Å / Num. all: 20597 / Num. obs: 20251 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.065 / Χ2: 1.002 / Net I/σ(I): 17.2
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.375 / Num. unique all: 1050 / Χ2: 1.011 / % possible all: 76.8

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.93 Å27.63 Å
Translation1.93 Å27.63 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.932→50.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.452 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2073 10.2 %RANDOM
Rwork0.203 ---
obs0.283 20228 98.17 %-
all-20597 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2---1.76 Å20 Å2
3---3.16 Å2
Refinement stepCycle: LAST / Resolution: 1.932→50.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 7 103 1837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211768
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.9752414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0055224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85323.33375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40815274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7871514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021334
X-RAY DIFFRACTIONr_nbd_refined0.1750.2752
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2127
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.26
X-RAY DIFFRACTIONr_mcbond_it0.2891.51164
X-RAY DIFFRACTIONr_mcangle_it0.47721823
X-RAY DIFFRACTIONr_scbond_it0.7813667
X-RAY DIFFRACTIONr_scangle_it1.194.5591
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 111 -
Rwork0.259 1116 -
obs-1227 82.24 %
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)
18.342-1.7732-7.51463.89652.607710.1813-0.0918-0.4624-0.14180.42810.0487-0.25390.09360.24780.0430.0605-0.0028-0.06870.06730.03910.02087.090411.396911.6279
238.2304-16.2043-6.42398.28154.12799.0401-0.3846-2.1199-0.04671.45410.3441-0.25040.69120.39940.04060.4766-0.051-0.10750.3160.00140.0215.787813.559724.882
32.2597-2.4003-6.1168.9649-5.428938.721-0.289-1.0261-0.00660.9503-0.105-0.91080.94651.7650.39390.22570.1107-0.15740.43230.02570.206216.10439.301117.6907
47.3299-1.5701-0.94894.78391.64383.3043-0.0528-0.609-0.00190.42890.0220.3401-0.3312-0.1060.03080.14170.0201-0.01710.0243-0.0194-0.0310.44520.537215.0555
521.0601-1.01751.20670.1315-0.83567.40390.2091-0.54421.03510.494-0.1083-0.0305-1.03650.4536-0.10080.354-0.0397-0.06790.1458-0.09160.1393.683126.715219.4046
610.5961-4.1448-8.57654.17674.065312.8956-0.0257-1.37750.41690.49650.3307-0.2622-0.13941.2803-0.3050.1995-0.0888-0.08520.2709-0.04830.121214.250619.640215.7612
72.4026-2.31810.73924.523-0.71012.7217-0.246-0.23440.41130.57580.1065-0.0655-0.41770.01470.13940.1043-0.0028-0.0429-0.0182-0.04860.0943-1.134225.87811.4294
82.5618-1.71911.187.91771.885.0316-0.0904-0.09460.62210.07120.167-0.5537-0.64940.3543-0.07660.0755-0.0073-0.05050.0064-0.01640.2225-0.227530.72156.0274
918.2201-17.765-0.350121.00170.85980.0798-1.1381-1.21920.75091.1580.887-0.36850.0262-0.00970.25110.05010.0051-0.06020.0522-0.03790.11559.134820.5403-0.1282
1010.9088-4.2579-4.50753.55321.36083.0695-0.1118-0.09810.22520.07980.08140.0695-0.086-0.02340.03040.00050.0101-0.041-0.0336-0.00120.0197-0.748619.58291.9308
1110.68755.9386-10.63585.3267-5.890613.45230.24750.19250.52530.1789-0.03450.4665-0.6313-0.3696-0.2130.02850.0425-0.06660.05610.0390.1594-9.244521.6727-1.2006
1224.585-3.02-2.67429.41080.18577.30920.12311.26751.4507-0.6909-0.13170.0965-0.47850.39740.00870.0866-0.0459-0.02140.09960.10370.04622.433419.5526-10.7746
134.3528-0.141-0.49163.52630.95623.9599-0.0455-0.16250.02250.1467-0.08590.67060.152-0.43550.13140.00240.0147-0.0298-0.0428-0.00190.083-7.37511.15472.9669
1421.3695.6596-6.15532.79910.590212.7102-0.43641.15050.452-0.32910.16770.7366-0.0583-0.61430.26880.06250.0174-0.10770.10170.05230.1372-10.15912.6831-7.2322
1530.4286-9.5439-0.904510.4246-1.254.88180.28841.9075-1.1754-0.8416-0.21350.68730.1236-0.5286-0.0750.1504-0.0308-0.06570.2048-0.00710.123-1.398911.0312-10.3092
163.43950.44280.32554.4843-0.09053.3185-0.0632-0.0506-0.03550.13880.02790.09020.0643-0.14840.0353-0.0113-0.0017-0.0165-0.00420.0020.0409-0.97119.70183.3332
172.66171.2922.492918.904516.512726.33560.0086-0.44690.21991.0369-0.52330.84440.0636-1.53890.51470.10060.00210.02960.1572-0.010.0842-5.43174.191410.5014
186.63690.01142.86794.3393-0.16969.8660.10320.047-0.03170.00670.03710.2344-0.1940.0233-0.1403-0.0301-0.00040.009-0.0590.008-0.0552-2.83485.96182.146
199.5726-2.0133-7.37015.13592.038412.9436-0.0788-0.63590.28850.5770.213-0.3460.12260.3565-0.13420.0642-0.0301-0.05910.04670.02010.09878.50045.75138.4914
2010.03350.8565-8.52669.5992-2.553521.99460.0991-0.5394-0.23090.5291-0.0041-0.30530.18030.6306-0.0950.0413-0.0323-0.02830.0090.02060.07377.12541.93356.9095
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1110 - 3612 - 38
2237 - 4639 - 48
3347 - 5549 - 57
4456 - 7258 - 74
5573 - 7775 - 79
6678 - 9080 - 92
7791 - 10893 - 110
88109 - 119111 - 121
99120 - 124122 - 126
1010125 - 139127 - 141
1111140 - 151142 - 153
1212152 - 158154 - 160
1313159 - 187161 - 189
1414188 - 193190 - 195
1515194 - 199196 - 201
1616200 - 208202 - 210
1717209 - 214211 - 216
1818215 - 226217 - 228
1919227 - 256229 - 258
2020257 - 265259 - 267

+
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