[English] 日本語
Yorodumi
- PDB-2hds: AmpC beta-lactamase in complex with 4-Methanesulfonylamino benzoi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hds
TitleAmpC beta-lactamase in complex with 4-Methanesulfonylamino benzoic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / AmpC beta-lactamase fragment-based drug design
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / 4-[(METHYLSULFONYL)AMINO]BENZOIC ACID / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsBabaoglu, K. / Shoichet, B.K.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: Deconstructing fragment-based inhibitor discovery
Authors: Babaoglu, K. / Shoichet, B.K.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3779
Polymers79,1762
Non-polymers1,2017
Water19,9791109
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6716
Polymers39,5881
Non-polymers1,0835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7063
Polymers39,5881
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.238, 74.764, 98.050
Angle α, β, γ (deg.)90.00, 115.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2000-

HOH

DetailsThe biological unit is a monomer

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ampC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 1115 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-4MB / 4-[(METHYLSULFONYL)AMINO]BENZOIC ACID


Mass: 215.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H9NO4S
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1109 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.8M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 2.6 % / Av σ(I) over netI: 13.3 / Number: 697717 / Rmerge(I) obs: 0.041 / Χ2: 1.24 / D res high: 1.16 Å / D res low: 50 Å / Num. obs: 265508 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.55096.310.0322.2532.7
1.982.599.510.0331.8232.8
1.731.9899.610.0411.4122.8
1.571.7399.910.0571.2062.7
1.461.5799.910.0811.0972.7
1.381.4610010.1170.9862.7
1.311.3810010.1570.9072.7
1.251.3199.910.2030.8522.6
1.21.2599.710.2720.7962.5
1.161.29410.3280.7462
ReflectionResolution: 1.16→50 Å / Num. all: 265508 / Num. obs: 265508 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.041 / Χ2: 1.238 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.16-1.220.328251380.74694
1.2-1.252.50.272266500.79699.7
1.25-1.312.60.203267410.85299.9
1.31-1.382.70.157267930.907100
1.38-1.462.70.117268130.986100
1.46-1.572.70.081267841.09799.9
1.57-1.732.70.057267951.20699.9
1.73-1.982.80.041267691.41299.6
1.98-2.52.80.033268131.82399.5
2.5-502.70.032262122.25396.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4


Resolution: 1.16→20 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.677 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.128 13360 5 %RANDOM
Rwork0.108 ---
obs0.109 265478 98.82 %-
all-265478 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.432 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.06 Å2
2---0.04 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.16→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5853 0 76 1135 7064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226039
X-RAY DIFFRACTIONr_bond_other_d0.0020.025389
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.9548265
X-RAY DIFFRACTIONr_angle_other_deg3.763312624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6735731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68924.71276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72415974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5861530
X-RAY DIFFRACTIONr_chiral_restr0.1370.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026693
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021184
X-RAY DIFFRACTIONr_nbd_refined0.2780.21346
X-RAY DIFFRACTIONr_nbd_other0.2030.25667
X-RAY DIFFRACTIONr_nbtor_refined0.1990.23047
X-RAY DIFFRACTIONr_nbtor_other0.110.23546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2788
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.281
X-RAY DIFFRACTIONr_mcbond_it1.9831.53619
X-RAY DIFFRACTIONr_mcbond_other0.8991.51458
X-RAY DIFFRACTIONr_mcangle_it2.87625903
X-RAY DIFFRACTIONr_scbond_it3.76332544
X-RAY DIFFRACTIONr_scangle_it5.0474.52357
X-RAY DIFFRACTIONr_rigid_bond_restr1.834312158
X-RAY DIFFRACTIONr_sphericity_free12.60931136
X-RAY DIFFRACTIONr_sphericity_bonded4.505311254
LS refinement shellResolution: 1.16→1.187 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 898 -
Rwork0.22 17194 -
obs-18092 91.47 %

+
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