[English] 日本語
Yorodumi
- PDB-1qlw: The Atomic Resolution Structure of a Novel Bacterial Esterase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qlw
TitleThe Atomic Resolution Structure of a Novel Bacterial Esterase
ComponentsESTERASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE) / ESTERASE / ANISOTROPIC REFINEMENT / ATOMIC RESOLUTION / ALPHA/BETA HYDROLASE
Function / homology: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Carboxylesterase
Function and homology information
Biological speciesALCALIGENES SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.09 Å
AuthorsBourne, P.C. / Isupov, M.N. / Littlechild, J.A.
Citation
Journal: Structure / Year: 2000
Title: The Atomic Resolution Structure of a Novel Bacterial Esterase
Authors: Bourne, P.C. / Isupov, M.N. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Novel Bacterial Esterase
Authors: Bourne, P.C. / Isupov, M.N. / Littlechild, J.A.
History
DepositionSep 17, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ESTERASE
B: ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6625
Polymers71,3742
Non-polymers2883
Water12,881715
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-30.2 kcal/mol
Surface area26750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)134.730, 55.600, 110.200
Angle α, β, γ (deg.)90.00, 125.06, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99234, -0.02182, 0.12158), (-0.01218, -0.9622, -0.27207), (0.12292, -0.27147, 0.95457)
Vector: 51.80933, 5.28295, -2.50379)
DetailsBIOLOGICAL_UNIT: DIMERIC

-
Components

#1: Protein ESTERASE


Mass: 35686.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ALPHA/BETA HYDROLASE FOLD / Source: (gene. exp.) ALCALIGENES SP. (bacteria) / Production host: AGROBACTERIUM SP. (bacteria) / References: UniProt: Q7SIA5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growpH: 7 / Details: PH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Bourne, P.C., (1999) Acta Crystallogr.,Sect.D, 55, 915.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMTris-HCl1drop
41.5-1.6 Mammonium sulfate1reservoir
3ammonium sulfate1dropsaturated

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8373
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: BENT MIRROR
RadiationMonochromator: HAMBURG / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8373 Å / Relative weight: 1
ReflectionResolution: 1.09→28 Å / Num. obs: 274290 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.5
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 98.2
Reflection shell
*PLUS
% possible obs: 98.2 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.09→30 Å / SU B: 0.296 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025
Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.158 1356 0.5 %RANDOM
Rwork0.143 ---
obs-272934 99.4 %-
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å2-0.02 Å2
2---2.25 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 1.09→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 15 715 5588
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.62
X-RAY DIFFRACTIONp_mcangle_it2.33
X-RAY DIFFRACTIONp_scbond_it2.32
X-RAY DIFFRACTIONp_scangle_it3.23
X-RAY DIFFRACTIONp_plane_restr0.0240.025
X-RAY DIFFRACTIONp_chiral_restr0.1140.15
X-RAY DIFFRACTIONp_singtor_nbd0.1640.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.110.3
X-RAY DIFFRACTIONp_planar_tor5.67
X-RAY DIFFRACTIONp_staggered_tor12.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor38.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1429 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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