[English] 日本語
Yorodumi
- PDB-4l3u: Crystal structure of a DUF3571 family protein (ABAYE3784) from Ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l3u
TitleCrystal structure of a DUF3571 family protein (ABAYE3784) from Acinetobacter baumannii AYE at 1.95 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF1209 family protein / DUF 3571 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterised protein PF16133, DUF4844 / Protein of unknown function DUF4844 / DUF4844 superfamily / Domain of unknown function (DUF4844) / hypothetical protein mp506/mpn330, domain 1 / Up-down Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (ABAYE3784) from Acinetobacter baumannii AYE at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7202
Polymers15,6841
Non-polymers351
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.739, 61.739, 94.886
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

-
Components

#1: Protein Uncharacterized protein


Mass: 15684.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AYE / Gene: ABAYE3784 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B0V6M1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 20-157 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.8857.33THE STRUCTURE WAS SOLVED USING TWO WAVELENGTH MAD PHASES FROM ANOTHER CRYSTAL. THE PHASING CRYSTAL DIFFRACTED TO 2.2 A. THE CRYSTAL USED FOR REFINEMENT DIFFRACTED TO 1.95 A. BOTH CRYSTALS ARE MEROHEDRALLY TWINNED.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop420% polyethylene glycol 6000, 0.1M citric acid pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop420% polyethylene glycol 6000, 3% Sorbitol, 0.1M citric acid pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.210.918401
SYNCHROTRONSSRL BL12-220.7514,0.9792
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDOct 25, 2012KOHZU: Double Crystal Si(111)
DECTRIS PILATUS 6M2PIXELApr 1, 2013Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)MADMx-ray1
2double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9184011
20.75141
30.97921
Reflection twinOperator: h,-k,-l / Fraction: 0.28
ReflectionResolution: 1.95→47.443 Å / Num. all: 12983 / Num. obs: 12983 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.075 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-27.40.6991.170859630.699100
2-2.067.40.4621.668489240.462100
2.06-2.127.40.3492.165948930.349100
2.12-2.187.40.2792.765398870.279100
2.18-2.257.20.2622.762118570.262100
2.25-2.337.40.2023.660498210.202100
2.33-2.427.40.1455.160168170.145100
2.42-2.527.30.1275.655497570.127100
2.52-2.637.30.1126.453337280.112100
2.63-2.767.30.1056.752147110.105100
2.76-2.917.20.0917.149236820.091100
2.91-3.087.20.088.345806330.08100
3.08-3.37.10.0699.142015910.069100
3.3-3.567.10.05811.439375550.058100
3.56-3.96.70.04913.434435150.049100
3.9-4.367.10.04712.833394700.047100
4.36-5.047.60.05211.530804030.052100
5.04-6.177.60.04912.326863530.049100
6.17-8.727.50.0451320262710.045100
8.72-47.4436.80.04215.210401520.04298

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
PHENIX1.8.2refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→47.443 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 1.76 / Phase error: 30.5 / Stereochemistry target values: TWIN_LSQ_F
Details: 1. RIDING HYDROGENS WERE BUILT TO IMPROVE THE ANTIBUMPING RESTRAINTS BUT WERE EXCLUDED FROM F_CALC. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. RIDING HYDROGENS WERE BUILT TO IMPROVE THE ANTIBUMPING RESTRAINTS BUT WERE EXCLUDED FROM F_CALC. 2. 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. 3.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.5. DATA ARE MEROHEDRALLY TWINNED WITH TWIN LAW (H, -K, -L).THE REFINED TWIN FRACTION WAS 0.28. THE R-FREE TEST SET REFLECTIONS WERE CHOSEN IN THIN RESOLUTION SHELLS.
RfactorNum. reflection% reflection
Rfree0.2055 753 5.81 %
Rwork0.1735 --
obs0.1804 12959 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.72 Å2 / Biso mean: 35.443 Å2 / Biso min: 19.38 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 1 57 994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004954
X-RAY DIFFRACTIONf_angle_d0.6831294
X-RAY DIFFRACTIONf_chiral_restr0.039152
X-RAY DIFFRACTIONf_plane_restr0.002170
X-RAY DIFFRACTIONf_dihedral_angle_d11.985345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.953-2.1010.2581440.262384252894
2.101-2.30750.29171450.26352400254594
2.3075-2.630.24631460.20672353249994
2.63-3.2720.21121500.18232408255894
3.272-7.78060.18011680.13492395256393
Refinement TLS params.Method: refined / Origin x: 38.6739 Å / Origin y: 17.5633 Å / Origin z: 44.0442 Å
111213212223313233
T0.2626 Å2-0.011 Å20.0019 Å2-0.2127 Å20.0129 Å2--0.2126 Å2
L1.1158 °2-0.0046 °2-0.2455 °2-1.1508 °2-0.0833 °2--1.1523 °2
S-0.0031 Å °-0.0008 Å °-0.1039 Å °-0.1321 Å °-0.0336 Å °0.0578 Å °0.2201 Å °0.071 Å °0.0377 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 31 through 153 )

+
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://pdbjlc1.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