[English] 日本語
Yorodumi
- PDB-1htz: CRYSTAL STRUCTURE OF TEM52 BETA-LACTAMASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1htz
TitleCRYSTAL STRUCTURE OF TEM52 BETA-LACTAMASE
ComponentsBETA-LACTAMASE MUTANT TEM52
KeywordsHYDROLASE / Mutant form of beta-lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStevens, R.C. / Orencia, M.C.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Predicting the emergence of antibiotic resistance by directed evolution and structural analysis.
Authors: Orencia, M.C. / Yoon, J.S. / Ness, J.E. / Stemmer, W.P. / Stevens, R.C.
History
DepositionJan 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-LACTAMASE MUTANT TEM52
B: BETA-LACTAMASE MUTANT TEM52
C: BETA-LACTAMASE MUTANT TEM52
D: BETA-LACTAMASE MUTANT TEM52
E: BETA-LACTAMASE MUTANT TEM52
F: BETA-LACTAMASE MUTANT TEM52


Theoretical massNumber of molelcules
Total (without water)173,6526
Polymers173,6526
Non-polymers00
Water10,539585
1
A: BETA-LACTAMASE MUTANT TEM52


Theoretical massNumber of molelcules
Total (without water)28,9421
Polymers28,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE MUTANT TEM52


Theoretical massNumber of molelcules
Total (without water)28,9421
Polymers28,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BETA-LACTAMASE MUTANT TEM52


Theoretical massNumber of molelcules
Total (without water)28,9421
Polymers28,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BETA-LACTAMASE MUTANT TEM52


Theoretical massNumber of molelcules
Total (without water)28,9421
Polymers28,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: BETA-LACTAMASE MUTANT TEM52


Theoretical massNumber of molelcules
Total (without water)28,9421
Polymers28,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: BETA-LACTAMASE MUTANT TEM52


Theoretical massNumber of molelcules
Total (without water)28,9421
Polymers28,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.382, 88.382, 500.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
BETA-LACTAMASE MUTANT TEM52 / 3.5.2.6 HYDROLASE


Mass: 28941.998 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: PET30A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9R435, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG8K, 125 mM MgOAc, 25mM Na citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
216 %PEG80001reservoir
3125 mM1reservoirMgOAc
425 mMNa citrate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 1999 / Details: mirrors
RadiationMonochromator: ALS 5.0.2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 73211 / Num. obs: 69960 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 22.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 7.1 / % possible all: 80
Reflection
*PLUS
Num. measured all: 736906
Reflection shell
*PLUS
% possible obs: 80 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TEM

1tem


Resolution: 2.4→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: 5 of 6 molecules refined using NCS, 6th molecule different due to packing. Pseudo-6 fold symmetry, attempts to process data as hexagonal or rhombohedral were unsuccessful
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3575 5 %Random
Rwork0.217 ---
all0.217 73211 --
obs-69960 91 %-
Displacement parametersBiso mean: 51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12168 0 0 587 12755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.7
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.006

+
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