[English] 日本語
Yorodumi
- PDB-5d0e: Crystal Structure of an adenylyl cyclase Ma1120-Cat in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d0e
TitleCrystal Structure of an adenylyl cyclase Ma1120-Cat in complex with GTP and calcium from Mycobacterium avium
ComponentsCyclase
KeywordsLYASE / Adenylyl cyclase / GTP
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / adenylate cyclase activity / intracellular signal transduction / GTP binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Nucleotide cyclase, GGDEF 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Cyclase
Similarity search - Component
Biological speciesMycobacterium avium subsp. avium 10-9275 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsBharambe, N.G. / Barathy, D.V. / Suguna, K.
CitationJournal: Febs J. / Year: 2016
Title: Substrate specificity determinants of class III nucleotidyl cyclases
Authors: Bharambe, N.G. / Barathy, D.V. / Syed, W. / Visweswariah, S.S. / Cola sigmaf o, M. / Misquith, S. / Suguna, K.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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.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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 1.4Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms ...pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclase
B: Cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3377
Polymers39,1752
Non-polymers1,1625
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-52 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.590, 55.710, 55.270
Angle α, β, γ (deg.)90.00, 109.74, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cyclase


Mass: 19587.342 Da / Num. of mol.: 2 / Fragment: UNP residues 106-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. avium 10-9275 (bacteria)
Gene: O972_06080 / Plasmid: pPROExHT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V7LAR8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / 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 modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5 / Details: 0.1M HEPES, 30% (w/v) PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.48→27.1 Å / Num. obs: 50213 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.2
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 7 % / Rmerge(I) obs: 0.93 / % possible all: 99.1

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WP9

4wp9


Resolution: 1.48→27.095 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 2531 5.07 %
Rwork0.1889 --
obs0.1907 49966 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→27.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 67 321 2789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132612
X-RAY DIFFRACTIONf_angle_d0.8033525
X-RAY DIFFRACTIONf_dihedral_angle_d18.246958
X-RAY DIFFRACTIONf_chiral_restr0.045403
X-RAY DIFFRACTIONf_plane_restr0.003452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.479-1.50740.32921350.29842586X-RAY DIFFRACTION97
1.5074-1.53820.28471320.2662641X-RAY DIFFRACTION100
1.5382-1.57170.26531490.2562610X-RAY DIFFRACTION100
1.5717-1.60820.31381210.2532653X-RAY DIFFRACTION100
1.6082-1.64840.28861390.22832649X-RAY DIFFRACTION100
1.6484-1.6930.23741260.23442644X-RAY DIFFRACTION100
1.693-1.74280.25471530.22392666X-RAY DIFFRACTION100
1.7428-1.7990.24121490.21912617X-RAY DIFFRACTION100
1.799-1.86330.26771390.21052650X-RAY DIFFRACTION100
1.8633-1.93790.31751270.28862489X-RAY DIFFRACTION94
1.9379-2.02610.26571550.20232623X-RAY DIFFRACTION99
2.0261-2.13290.19121570.19712649X-RAY DIFFRACTION100
2.1329-2.26640.2411380.21252598X-RAY DIFFRACTION99
2.2664-2.44130.22151300.182656X-RAY DIFFRACTION99
2.4413-2.68680.20311620.17972649X-RAY DIFFRACTION100
2.6868-3.07510.2321380.17612684X-RAY DIFFRACTION100
3.0751-3.87250.20441440.15442660X-RAY DIFFRACTION100
3.8725-27.09920.18851370.15812711X-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)
15.6299-1.56580.32922.34240.24231.65850.0962-0.15260.15760.0376-0.11640.1526-0.2348-0.24550.01750.18330.01290.01450.13690.01040.134217.0421-38.0243139.7698
22.33640.1716-0.48242.66990.1843.02270.0271-0.17970.06120.19410.01-0.0388-0.0586-0.075-0.0240.12350-0.0160.10460.0010.125326.716-47.4247141.1543
34.34070.3919-0.40584.70812.93692.23110.118-0.102-0.29990.2411-0.1220.0190.3452-0.30060.02460.1757-0.004-0.02930.10580.03620.214123.9209-60.543138.256
46.1019-3.38490.1064.5426-0.91670.73970.0624-0.01210.1716-0.2913-0.0047-0.0682-0.00010.0307-0.04650.162-0.0255-0.03610.1321-0.02980.081822.4439-42.9959117.9709
56.7332-1.6588-1.62017.36053.13886.50560.08390.14580.1345-0.41350.1643-0.1294-0.21040.2875-0.19080.1836-0.0616-0.00610.18750.04360.169315.9677-37.9187113.6733
63.6339-0.4168-0.70422.40440.82664.2553-0.03110.1339-0.0514-0.1787-0.00820.1806-0.0367-0.24560.04170.13260.0188-0.02940.16290.01870.21745.1498-41.7672118.7378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 102 through 147 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 251 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 270 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 103 through 147 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 148 through 184 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 185 through 271 )B0

+
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