[English] 日本語
Yorodumi
- PDB-4y0t: Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y0t
TitleCrystal structure of apo form of OXA-58, a Carbapenem hydrolyzing Class D beta-lactamase from Acinetobacter baumanii (P21, 4mol/ASU)
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class D beta-lactamase / OXA-58 / 4mol/ASU
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase OXA-58
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPratap, S. / Katiki, M. / Gill, P. / Golemi-Kotra, D. / Kumar, P.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2015
Title: Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D beta-Lactamase of Acinetobacter baumannii.
Authors: Pratap, S. / Katiki, M. / Gill, P. / Kumar, P. / Golemi-Kotra, D.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)125,9934
Polymers125,9934
Non-polymers00
Water6,990388
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.017, 65.095, 191.964
Angle α, β, γ (deg.)90.00, 91.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERKCXKCXAA38 - 8638 - 86
21SERSERKCXKCXDD38 - 8638 - 86
12ILEILETYRTYRAA87 - 27987 - 279
22ILEILETYRTYRDD87 - 27987 - 279

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Beta-lactamase


Mass: 31498.209 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-58, bla-oxa-58, bla-oxa58 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2TR58, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 32.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris base/Hydrochloric acid (pH 8.0) and 28% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.29→34.79 Å / Num. obs: 37470 / % possible obs: 91.23 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.15
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / % possible all: 74.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.3→34.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 20.364 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.765 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24328 1847 4.9 %RANDOM
Rwork0.19414 ---
obs0.19651 35622 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.54 Å2
2--0.87 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 0 388 8128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197934
X-RAY DIFFRACTIONr_bond_other_d0.0080.027601
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.94710720
X-RAY DIFFRACTIONr_angle_other_deg1.349317462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64824.883383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.764151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1441536
X-RAY DIFFRACTIONr_chiral_restr0.0860.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029016
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021880
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1891.8933868
X-RAY DIFFRACTIONr_mcbond_other1.1881.8933867
X-RAY DIFFRACTIONr_mcangle_it1.9842.8364825
X-RAY DIFFRACTIONr_mcangle_other1.9842.8364826
X-RAY DIFFRACTIONr_scbond_it1.3342.0074066
X-RAY DIFFRACTIONr_scbond_other1.3342.0074067
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2292.9545893
X-RAY DIFFRACTIONr_long_range_B_refined4.93615.4149128
X-RAY DIFFRACTIONr_long_range_B_other4.90615.249063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2460 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2D
LS refinement shellResolution: 2.296→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 84 -
Rwork0.305 1837 -
obs--63.84 %
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)
12.6606-0.69611.3281.6075-0.97223.940.0301-0.02810.20710.1664-0.0654-0.063-0.06980.22540.03530.049-0.0180.0510.33090.00220.1095-3.11.30374.161
24.83261.3668-0.68638.03970.94214.61390.09410.1894-0.52760.00420.00630.06170.5876-0.0052-0.10040.12760.0172-0.00440.4463-0.00930.1286-14.85-7.62753.66
32.1453-0.4770.39231.9704-1.39792.91140.07290.02390.0351-0.02160.00390.00160.0245-0.075-0.07680.0154-0.0190.00040.396-0.01990.0611-8.3050.94569.313
47.91823.9912.22894.4199-0.036511.49890.02320.3205-0.2254-0.2917-0.0271-0.52310.11960.00280.0040.2130.03210.0160.40850.0110.2075-59.67156.79237.616
54.53761.2367-1.66672.2627-0.73233.1015-0.19790.1216-0.1951-0.13840.0883-0.2880.0510.33810.10970.04290.04330.00410.37290.00410.1168-59.64553.16924.206
62.4084-0.72240.13560.84311.13592.4107-0.14070.2069-0.03610.1193-0.0390.1030.1416-0.26730.17970.1347-0.02820.02720.5629-0.01080.0173-43.14856.6575.629
77.13614.35752.61848.65240.50183.5679-0.3768-0.5631.14150.567-0.3198-0.3662-0.6117-0.20710.69660.22080.0819-0.15870.4668-0.00450.5624-42.65374.044.202
82.7678-0.5086-0.93853.28170.62132.0029-0.1832-0.14110.02740.0870.057-0.0650.03260.08870.12620.10960.004-0.0150.3755-0.01090.0211-47.84657.7613.658
94.0104-1.687-2.432.7775-0.51327.1661-0.1462-0.20220.30160.24790.0146-0.2745-0.1350.28330.13160.0677-0.004-0.03640.35490.00520.0943-56.76457.4036.345
109.0772-0.2117-3.68923.14040.83116.8845-0.23670.1907-0.35920.1322-0.06560.03150.5032-0.15020.30220.1624-0.03410.00890.3221-0.01670.0405-41.92748.33414.493
115.55580.4761-0.78232.4724-0.81340.4522-0.14430.24260.24250.09040.11380.088-0.0827-0.05970.03050.104-0.0043-0.01110.37430.01710.1187-46.2860.18620.803
123.43362.2518-1.00536.72141.37383.4327-0.3598-0.17680.1771-0.41430.0953-0.1772-0.5220.05690.26440.18440.0323-0.09680.36760.06720.1554-54.03961.18323.523
136.10013.69365.43493.62641.00668.7213-0.45770.12080.3591-0.31240.17590.1369-0.4417-0.10260.28170.12720.08010.10770.50320.08290.2608-49.93861.46131.926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 101
2X-RAY DIFFRACTION2A102 - 141
3X-RAY DIFFRACTION3A142 - 279
4X-RAY DIFFRACTION4D38 - 50
5X-RAY DIFFRACTION5D51 - 81
6X-RAY DIFFRACTION6D82 - 101
7X-RAY DIFFRACTION7D102 - 121
8X-RAY DIFFRACTION8D122 - 161
9X-RAY DIFFRACTION9D162 - 181
10X-RAY DIFFRACTION10D182 - 201
11X-RAY DIFFRACTION11D202 - 241
12X-RAY DIFFRACTION12D242 - 261
13X-RAY DIFFRACTION13D262 - 279

+
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