[English] 日本語
Yorodumi
- PDB-2wq5: Non-antibiotic properties of tetracyclines: structural basis for ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wq5
TitleNon-antibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2.
ComponentsPHOSPHOLIPASE A2, ACIDIC
KeywordsHYDROLASE / MINOCYCLINE / PHOSPHOLIPASE / METAL-BINDING / LIPID DEGRADATION / CALCIUM BINDING LOOP / CARBOXYLIC ESTER HYDROLASE
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MIY / Acidic phospholipase A2 2
Similarity search - Component
Biological speciesNAJA NAJA (Indian cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDalm, D. / Palm, G.J. / Hinrichs, W.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Non-Antibiotic Properties of Tetracyclines: Structural Basis for Inhibition of Secretory Phospholipase A(2).
Authors: Dalm, D. / Palm, G.J. / Aleksandrov, A. / Simonson, T. / Hinrichs, W.
History
DepositionAug 13, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: PHOSPHOLIPASE A2, ACIDIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9504
Polymers13,3561
Non-polymers5943
Water3,009167
1
A: PHOSPHOLIPASE A2, ACIDIC
hetero molecules

A: PHOSPHOLIPASE A2, ACIDIC
hetero molecules

A: PHOSPHOLIPASE A2, ACIDIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,84912
Polymers40,0683
Non-polymers1,7819
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
Buried area7220 Å2
ΔGint-80 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.712, 68.712, 68.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1001-

CA

21A-2005-

HOH

31A-2006-

HOH

41A-2011-

HOH

51A-2165-

HOH

61A-2166-

HOH

-
Components

#1: Protein PHOSPHOLIPASE A2, ACIDIC / PHOSPHOLIPASE A2 / PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE


Mass: 13356.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) NAJA NAJA (Indian cobra) / Organ: VENOM SACK / References: UniProt: P15445, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE


Mass: 457.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O7 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN PURIFIED FROM NATURAL SOURCE. CONFLICTS BELOW ARE REPORTED AS NATURAL VARIANTS BY THIS AUTHOR.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.5 % / Description: NONE
Crystal growDetails: 26% PEG 4000, 0.24M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Jan 10, 2008 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→34.4 Å / Num. obs: 13314 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3D

1a3d


Resolution: 1.65→34.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.895 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 638 4.8 %RANDOM
Rwork0.189 ---
obs0.191 12547 99.3 %-
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: 28.78 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 39 167 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211012
X-RAY DIFFRACTIONr_bond_other_d0.0020.02677
X-RAY DIFFRACTIONr_angle_refined_deg1.4592.0061387
X-RAY DIFFRACTIONr_angle_other_deg0.9053.0171617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7495122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66724.37548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96315149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.062155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.2570.2269
X-RAY DIFFRACTIONr_nbd_other0.1920.2759
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2525
X-RAY DIFFRACTIONr_nbtor_other0.090.2498
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0180.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8061.5615
X-RAY DIFFRACTIONr_mcbond_other0.2431.5250
X-RAY DIFFRACTIONr_mcangle_it1.2642961
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8373471
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5174.5426
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 46 -
Rwork0.26 899 -
obs--99.26 %
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)
16.1026-0.5902-0.98362.01240.36383.26760.1271-0.21610.26360.042-0.0248-0.0981-0.07030.2953-0.10230.0135-0.0170.01250.0249-0.0023-0.0346-8.19285.39323.5886
20.76590.8689-2.5222.7678-2.54168.36220.2596-0.10490.31730.76390.09740.2581-0.85870.003-0.35710.16910.04990.09410.0194-0.00740.0042-4.981812.792216.3823
312.27095.93415.85145.70495.352617.42010.2052-0.17380.4386-0.33730.23680.8938-1.0169-1.1283-0.4420.03760.05960.07170.07280.07660.099-12.199411.36358.017
44.15061.8306-2.87251.2356-1.1052.1294-0.07060.40220.128-0.09190.09770.0506-0.0003-0.2323-0.0270.03570.0078-0.00810.06280.00930.0103-10.14064.63176.7527
54.8498-0.06660.77081.2496-0.39622.67080.0288-0.2268-0.27420.1132-0.02930.05140.15770.01260.00040.0206-0.00610.022-0.02740.0095-0.0079-17.4744-1.903621.697
61.7990.4184-1.19650.7792-0.78392.05020.11340.02290.05480.0443-0.0535-0.008-0.10510.0527-0.05990.01470.02550.0149-0.0232-0.0114-0.0309-7.10677.737711.2511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 26
3X-RAY DIFFRACTION3A27 - 32
4X-RAY DIFFRACTION4A33 - 53
5X-RAY DIFFRACTION5A54 - 83
6X-RAY DIFFRACTION6A84 - 119

+
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