[English] 日本語
Yorodumi
- PDB-4dw8: Crystal structure of a haloacid dehalogenase-like hydrolase (Targ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dw8
TitleCrystal structure of a haloacid dehalogenase-like hydrolase (Target EFI-900331) from Bacteroides thetaiotaomicron with bound Na crystal form I
ComponentsHaloacid dehalogenase-like hydrolase
KeywordsHYDROLASE / HAD / putative phosphatase / Enzyme Function Initiative / EFI / Structural Genomics
Function / homology
Function and homology information


phosphatase activity / magnesium ion binding / cytosol
Similarity search - Function
Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical cof family signature 2. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical cof family signature 2. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Haloacid dehalogenase-like hydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsVetting, M.W. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Allen, K.N. / Dunaway-Mariano, D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a haloacid dehalogenase-like hydrolase (Target EFI-900331) from Bacteroides thetaiotaomicron with bound Na crystal form I
Authors: Vetting, M.W. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Allen, K.N. / Dunaway-Mariano, D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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: Haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2245
Polymers31,2011
Non-polymers234
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.669, 73.133, 82.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Haloacid dehalogenase-like hydrolase


Mass: 31200.725 Da / Num. of mol.: 1
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_3352 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8A2F3, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.75
Details: protein solution: 10 mM HEPES, pH 7.8, 150 mM sodium chloride, 10% glycerol, 5 mM magnesium, reservoir solution: 20% PEG4000, 100 mM sodium acetate, pH 4.75, 200 mM ammonium acetate, 12% ...Details: protein solution: 10 mM HEPES, pH 7.8, 150 mM sodium chloride, 10% glycerol, 5 mM magnesium, reservoir solution: 20% PEG4000, 100 mM sodium acetate, pH 4.75, 200 mM ammonium acetate, 12% ethylene glycol, cryoprotectant: reservoir solution + 10% glycerol + 10% ethylene glycol + 200 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 1, 2011 / Details: mirrors
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 42541 / Num. obs: 42541 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Χ2: 1.137 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.536.20.44920771.043199.4
1.53-1.556.20.39221321.034199.4
1.55-1.586.20.33120721.061199.4
1.58-1.626.20.28721181.058199.5
1.62-1.656.20.23320871.066199.7
1.65-1.696.20.20421301.047199.4
1.69-1.736.20.17121041.051199.8
1.73-1.786.20.14121151.02199.4
1.78-1.836.20.12321181.036199.6
1.83-1.896.20.10321311.057199.6
1.89-1.966.40.10221001.303199.7
1.96-2.046.50.10521561.249199.8
2.04-2.136.60.11521261.2851100
2.13-2.246.80.11421511.4311100
2.24-2.3870.11221421.4661100
2.38-2.567.20.08921731.0291100
2.56-2.827.30.05221741.1231100
2.82-3.237.30.03921771.2321100
3.23-4.0770.0321941.02198.7
4.07-4060.02520641.038188

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NIW

3niw


Resolution: 1.502→20.281 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8756 / SU ML: 0.12 / σ(F): 0 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1906 4.67 %RANDOM
Rwork0.181 ---
all0.1824 40830 --
obs0.1824 40830 95.1 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.686 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 56.72 Å2 / Biso mean: 23.8647 Å2 / Biso min: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1-4.9275 Å2-0 Å2-0 Å2
2---2.059 Å2-0 Å2
3----2.8684 Å2
Refinement stepCycle: LAST / Resolution: 1.502→20.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 4 232 2313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132193
X-RAY DIFFRACTIONf_angle_d1.4552987
X-RAY DIFFRACTIONf_chiral_restr0.1347
X-RAY DIFFRACTIONf_plane_restr0.007388
X-RAY DIFFRACTIONf_dihedral_angle_d11.848840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.502-1.53930.24131260.21242515264188
1.5393-1.58090.24841290.2042632276191
1.5809-1.62740.23181230.18722648277192
1.6274-1.67990.20721360.1792672280893
1.6799-1.740.20621370.16792715285294
1.74-1.80960.18781310.16972705283694
1.8096-1.89190.21161340.16732757289195
1.8919-1.99150.2081380.1752835297397
1.9915-2.11620.20551410.17792881302299
2.1162-2.27940.18231420.17282900304299
2.2794-2.50840.20961430.18432912305599
2.5084-2.87050.19561430.19312922306599
2.8705-3.61320.24281440.182429733117100
3.6132-20.28290.20491390.17892857299691
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)
14.24460.01620.90763.95120.93093.84670.05050.3724-0.1197-0.26650.05480.19110.25680.206-0.07110.19910.0168-0.00520.15070.0070.116-14.4544-19.1511-30.1096
21.43110.02840.5061.3868-1.09463.19720.16380.15710.0402-0.1384-0.0462-0.17080.06860.5348-0.11590.12090.02580.00780.1846-0.02820.1384-4.4262-21.4944-17.8543
31.89970.5638-0.36523.62530.67442.31970.0941-0.1874-0.00150.1989-0.14250.05730.14120.03730.04860.07810.0017-0.02760.11270.00140.1036-13.4325-31.654-2.8635
41.93180.7065-0.28862.7536-2.49985.148-0.09580.09040.39230.2503-0.0891-0.2535-0.80480.30640.03650.1746-0.0474-0.04660.154-0.01050.2545-6.7799-8.4382-15.8642
52.8162-1.10351.19043.95010.61783.3696-0.0885-0.136-0.01030.2330.04410.2090.0848-0.19690.03830.16470.00830.01130.11430.0190.1462-21.7225-11.4096-24.159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:35)A2 - 35
2X-RAY DIFFRACTION2(chain A and resid 36:95)A36 - 95
3X-RAY DIFFRACTION3(chain A and resid 96:190)A96 - 190
4X-RAY DIFFRACTION4(chain A and resid 191:214)A191 - 214
5X-RAY DIFFRACTION5(chain A and resid 215:267)A215 - 267

+
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