[English] 日本語
Yorodumi
- PDB-4hf7: Crystal structure of a GDSL-like lipase (BT0569) from Bacteroides... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hf7
TitleCrystal structure of a GDSL-like lipase (BT0569) from Bacteroides thetaiotaomicron VPI-5482 at 1.77 A resolution
ComponentsPutative acylhydrolase
KeywordsHYDROLASE / PF13472 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologySGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative acylhydrolase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.77 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a GDSL-like lipase (BT0569) from Bacteroides thetaiotaomicron VPI-5482 at 1.77 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative acylhydrolase


Theoretical massNumber of molelcules
Total (without water)23,6891
Polymers23,6891
Non-polymers00
Water4,666259
1
A: Putative acylhydrolase

A: Putative acylhydrolase


Theoretical massNumber of molelcules
Total (without water)47,3792
Polymers47,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area1590 Å2
ΔGint-11 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.201, 110.680, 88.776
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

-
Components

#1: Protein Putative acylhydrolase


Mass: 23689.252 Da / Num. of mol.: 1 / Fragment: UNP residues 29-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0569, NP_809482.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8AA96
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 29-236) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 29-236) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.40M ammonium sulfate, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97876,0.97932
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978761
30.979321
ReflectionResolution: 1.77→46.47 Å / Num. obs: 24579 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.59 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.77-1.830.5992.378602300198.5
1.83-1.910.46388982654198.3
1.91-1.990.326472172229198.4
1.99-2.10.2215.479662518197
2.1-2.230.1866.782482415198.8
2.23-2.40.1478.281352433198.5
2.4-2.640.1179.477442457198.5
2.64-3.020.08612.985012487198.8
3.02-3.810.0561880322514198.2
3.81-46.470.04421.581112580197

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.77→46.47 Å / Cor.coef. Fo:Fc: 0.8857 / Cor.coef. Fo:Fc free: 0.8733 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. EXPERIMENTAL (MAD) PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. RESIDUE SER62 WAS MODELED AS A O-SULFO-L-SERINE (OSE) BASED ON THE FIT TO DENSITY AND PRESENCE OF 2.4 M AMMONIUM SULFATE IN THE CRYSTALLIZATION CONDITION. LIQUID CHROMATOGRAPHY - MASS SPECTROMETRY DATA FROM THE PROTEIN PRIOR TO CRYSTALLIZATION DID NOT SHOW ANY EVIDENCE OF MODIFICATION. NOTE THAT PHOSPHOSERINE (SEP) WOULD ALSO FIT THE DENSITY AND CANNOT BE RULED OUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1236 5.04 %RANDOM
Rwork0.1962 ---
obs0.1973 24538 98.22 %-
Displacement parametersBiso max: 75.93 Å2 / Biso mean: 18.1164 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1-4.9273 Å20 Å20 Å2
2--4.607 Å20 Å2
3----9.5344 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.77→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 0 259 1876
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d784SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes246HARMONIC5
X-RAY DIFFRACTIONt_it1678HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion222SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2264SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1678HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2282HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion2.78
LS refinement shellResolution: 1.77→1.85 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2255 139 4.67 %
Rwork0.2236 2836 -
all0.2237 2975 -
obs--98.22 %
Refinement TLS params.Method: refined / Origin x: 2.5815 Å / Origin y: 39.5642 Å / Origin z: 47.4086 Å
111213212223313233
T0.0254 Å2-0.0056 Å2-0.0037 Å2--0.0432 Å20.0055 Å2---0.0719 Å2
L0.5809 °2-0.0632 °2-0.1132 °2-0.6205 °20.0071 °2--0.0884 °2
S-0.0251 Å °0.012 Å °-0.0158 Å °0.0134 Å °0.0441 Å °-0.0094 Å °0.0207 Å °-0.0114 Å °-0.019 Å °
Refinement TLS groupSelection details: { A|32 - A|236 }

+
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