[English] 日本語
Yorodumi
- PDB-3pl0: Crystal structure of a bsmA homolog (Mpe_A2762) from Methylobium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pl0
TitleCrystal structure of a bsmA homolog (Mpe_A2762) from Methylobium petroleophilum PM1 at 1.91 A resolution
ComponentsUncharacterized protein
KeywordsBIOSYNTHETIC PROTEIN / QUORUM SENSING / BIOFILM FORMATION / DOUBLE-STRANDED BETA-HELIX FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology2OG-Fe dioxygenase / 2OG-Fe dioxygenase / q2cbj1_9rhob like domain / dioxygenase activity / Jelly Rolls / Sandwich / Mainly Beta / 2OG-Fe dioxygenase family protein
Function and homology information
Biological speciesMethylibium petroleiphilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site.
Authors: Xu, Q. / Grant, J. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Miller, M.D. / Lesley, S.A. / Godzik, A. / Elsliger, M.A. / Deacon, A.M. / Wilson, I.A.
History
DepositionNov 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Sep 24, 2014Group: Database references
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
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4124
Polymers57,2852
Non-polymers1282
Water7,440413
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7703
Polymers28,6421
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,6421
Polymers28,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.508, 63.203, 104.504
Angle α, β, γ (deg.)90.000, 97.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 0 - 253 / Label seq-ID: 1 - 254

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Uncharacterized protein


Mass: 28642.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylibium petroleiphilum (bacteria) / Strain: PM1 / Gene: Mpe_A2762 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A2SJH7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.49 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.90M lithium chloride, 6.00% polyethylene glycol 6000, 0.1M HEPES pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
30.97931
ReflectionResolution: 1.91→28.923 Å / Num. obs: 43643 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.356 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.5431.9138668670197.6
1.98-2.060.3892.6134418415198.4
2.06-2.150.2853.5129158084197.9
2.15-2.260.1974.9132038236197.7
2.26-2.410.1416.5143618974198.2
2.41-2.590.1048.4130448126198.1
2.59-2.850.06711.4134868412197.4
2.85-3.260.03917.1130848209195.7
3.26-4.10.02822.9126057970192.6
4.1-28.9230.02226.4130258095192.6

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→28.923 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.692 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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. GLYCEROL (GOL) AND CHLORIDE (CL) MODELED ARE PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 2199 5 %RANDOM
Rwork0.1694 ---
obs0.1715 43627 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.69 Å2 / Biso mean: 35.7943 Å2 / Biso min: 15.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-0.46 Å2
2--2.22 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.91→28.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 7 413 4391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214236
X-RAY DIFFRACTIONr_bond_other_d0.0010.022904
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9535803
X-RAY DIFFRACTIONr_angle_other_deg0.89337034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80122.823209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26815651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9321540
X-RAY DIFFRACTIONr_chiral_restr0.090.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02909
X-RAY DIFFRACTIONr_mcbond_it1.89932582
X-RAY DIFFRACTIONr_mcbond_other0.77831041
X-RAY DIFFRACTIONr_mcangle_it2.91254168
X-RAY DIFFRACTIONr_scbond_it4.81681654
X-RAY DIFFRACTIONr_scangle_it6.735111616
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3217 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL10.5
MEDIUM THERMAL1.372
LS refinement shellResolution: 1.905→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 155 -
Rwork0.295 2961 -
all-3116 -
obs--97.25 %
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)
11.3105-0.0298-0.3110.8985-0.23440.7279-0.01780.1264-0.0087-0.04410.0203-0.0066-0.0337-0.0617-0.00250.06090.01910.01280.11580.01010.0032-7.571626.04267.2541
21.21940.44730.01950.7604-0.1330.74580.07820.0851-0.07480.0419-0.0793-0.04580.01370.00770.00110.05770.0221-0.0330.037-0.00290.0812-9.2961-2.32490.057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 253
2X-RAY DIFFRACTION2B0 - 253

+
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