[English] 日本語
Yorodumi
- PDB-3ba3: Crystal structure of Pyridoxamine 5'-phosphate oxidase-like prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ba3
TitleCrystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution
ComponentsPyridoxamine 5'-phosphate oxidase-like protein
KeywordsOXIDOREDUCTASE / NP_783940.1 / Pyridoxamine 5'-phosphate oxidase-like protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyElectron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Pyridoxamine 5'-phosphate oxidase family protein, FMN-binding / :
Function and homology information
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyridoxamine 5'-phosphate oxidase-like protein
B: Pyridoxamine 5'-phosphate oxidase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,22714
Polymers32,4142
Non-polymers81312
Water7,440413
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.379, 137.379, 137.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11B-153-

HOH

21B-236-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Pyridoxamine 5'-phosphate oxidase-like protein / Protein lp_0091


Mass: 16206.972 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarumLactiplantibacillus plantarum
Strain: WCFS1, NCIMB 8826 / Gene: NP_783940.1, lp_0091 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q890D6, UniProt: F9USS0*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. REMARK 999

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NANODROP, 2.0M (NH4)2SO4, 0.2M Li2SO4, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97971
ReflectionResolution: 1.55→29.975 Å / Num. obs: 64534 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.55-1.599.20.9130.94305046870.913100
1.59-1.639.60.74814410446000.748100
1.63-1.689.90.6181.34361244130.618100
1.68-1.7310.10.5041.64392043390.504100
1.73-1.7910.30.3772.14319642000.377100
1.79-1.8510.40.2772.84253440760.277100
1.85-1.9210.50.2123.64100239140.212100
1.92-210.50.164.63996638080.16100
2-2.0910.50.1295.63842536670.129100
2.09-2.1910.50.1046.73626034590.104100
2.19-2.3110.40.0897.73469233300.089100
2.31-2.4510.40.088.43290831590.08100
2.45-2.6210.30.0798.13075729800.079100
2.62-2.8310.30.087.62863727860.08100
2.83-3.110.10.0787.42610925830.078100
3.1-3.479.80.0668.92286223440.066100
3.47-49.20.04811.31927420960.048100
4-4.910.30.044111859518020.044100
4.9-6.9310.20.04211.41469314350.042100
6.93-29.9759.30.03912.979628560.03998.8

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.55→29.975 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.192 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE ION FROM THE CRYSTALLIZATION CONDITIONS AND ETHYLENE GLYCOL FROM THE CRYO CONDITIONS ARE MODELED IN THE STRUCTURE. 5. UNKNOWN ELECTRON DENSITY NEAR RESIDUE 18 IN SUBUNIT A AND RESIDUE 14 IN SUBUNIT B IS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3263 5.1 %RANDOM
Rwork0.17 ---
obs0.171 64447 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.142 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 50 413 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222463
X-RAY DIFFRACTIONr_bond_other_d0.0020.021565
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9683374
X-RAY DIFFRACTIONr_angle_other_deg0.98733880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98626.346104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12715393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.262154
X-RAY DIFFRACTIONr_chiral_restr0.1010.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022771
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02449
X-RAY DIFFRACTIONr_nbd_refined0.2440.2526
X-RAY DIFFRACTIONr_nbd_other0.1970.21670
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21253
X-RAY DIFFRACTIONr_nbtor_other0.0880.21235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.233
X-RAY DIFFRACTIONr_mcbond_it2.27431662
X-RAY DIFFRACTIONr_mcbond_other0.5953605
X-RAY DIFFRACTIONr_mcangle_it2.89452536
X-RAY DIFFRACTIONr_scbond_it4.47281006
X-RAY DIFFRACTIONr_scangle_it6.06511838
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 252 -
Rwork0.243 4424 -
all-4676 -
obs--100 %
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)
11.3051.17450.03842.6353-0.28161.37520.0354-0.0732-0.13410.1642-0.0775-0.37120.0175-0.03490.0422-0.0516-0.0143-0.0569-0.0808-0.0069-0.033978.666103.76846.2
20.87130.3751-0.08180.7710.28050.94380.0494-0.05640.04090.0521-0.04190.0672-0.0126-0.0325-0.0075-0.05280.0006-0.0078-0.0638-0.0041-0.047356.49599.83438.136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1432 - 144
2X-RAY DIFFRACTION2BB1 - 1442 - 145

+
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