[English] 日本語
Yorodumi
- PDB-9eid: A broad-substrate spectrum lactate racemase A from Isosphaera pal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eid
TitleA broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with D-2-Hydroxybutyrate
ComponentsA broad-substrate spectrum lactate racemase A
KeywordsISOMERASE / Catalytic activity / isomerase activity / racemase and epimerase activity racemase acting on hydroxy acids and derivatives
Function / homology
Function and homology information


lactate racemase activity
Similarity search - Function
: / : / Lactate racemase C-terminal domain / LarA-like, C-terminal domain / LarA-like, N-terminal / : / Lactate racemase N-terminal domain
Similarity search - Domain/homology
Chem-4EY / NICKEL (II) ION / PHOSPHATE ION / (2R)-2-oxidanylbutanoic acid / Uncharacterized protein
Similarity search - Component
Biological speciesIsosphaera pallida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsGatreddi, S. / Hausinger, R.P. / Hu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140931 United States
CitationJournal: Biorxiv / Year: 2024
Title: Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum.
Authors: Gatreddi, S. / Urdiain-Arraiza, J. / Desguin, B. / Hausinger, R.P. / Hu, J.
History
DepositionNov 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: A broad-substrate spectrum lactate racemase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6066
Polymers45,8571
Non-polymers7495
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.725, 79.613, 104.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein A broad-substrate spectrum lactate racemase A


Mass: 45856.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Isosphaera pallida (bacteria) / Gene: Isop_3476 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ3900 / References: UniProt: E8QWZ4

-
Non-polymers , 5 types, 533 molecules

#2: Chemical ChemComp-UCU / (2R)-2-oxidanylbutanoic acid / (R)-2-Hydroxybutanoic acid


Mass: 104.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4EY / 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium / Dithiodinicotinic acid mononucleotide


Mass: 396.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO8PS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris buffer pH 6.0, 25% PEG 5000, and 2.8 mM Sodium D/L-2-hydroxybutyrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.38→29.11 Å / Num. obs: 80218 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.099 / Net I/σ(I): 18.6
Reflection shellResolution: 1.38→1.41 Å / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3732 / CC1/2: 0.805 / Rpim(I) all: 0.288 / Rrim(I) all: 0.818

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→29.11 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1662 3987 4.98 %
Rwork0.1513 --
obs0.1521 80127 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 42 528 3769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063410
X-RAY DIFFRACTIONf_angle_d0.994691
X-RAY DIFFRACTIONf_dihedral_angle_d19.343491
X-RAY DIFFRACTIONf_chiral_restr0.088557
X-RAY DIFFRACTIONf_plane_restr0.006609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.23751350.21722550X-RAY DIFFRACTION94
1.4-1.420.22861480.2022638X-RAY DIFFRACTION98
1.42-1.440.18211300.1912646X-RAY DIFFRACTION100
1.44-1.460.22341550.17792707X-RAY DIFFRACTION100
1.46-1.480.18321670.16922673X-RAY DIFFRACTION100
1.48-1.50.15561270.16262698X-RAY DIFFRACTION100
1.5-1.520.17061570.15772662X-RAY DIFFRACTION100
1.52-1.550.22871310.15232735X-RAY DIFFRACTION100
1.55-1.580.18631310.152690X-RAY DIFFRACTION100
1.58-1.60.17311520.14832678X-RAY DIFFRACTION100
1.6-1.630.17541230.14532711X-RAY DIFFRACTION100
1.63-1.670.16571370.14592748X-RAY DIFFRACTION100
1.67-1.70.1571430.14012678X-RAY DIFFRACTION100
1.7-1.740.16961290.14412737X-RAY DIFFRACTION100
1.74-1.790.16491310.1452716X-RAY DIFFRACTION100
1.79-1.840.16221290.14832720X-RAY DIFFRACTION100
1.84-1.890.16341410.15372716X-RAY DIFFRACTION100
1.89-1.950.18661360.15182744X-RAY DIFFRACTION100
1.95-2.020.18611440.15012722X-RAY DIFFRACTION100
2.02-2.10.15941700.14932698X-RAY DIFFRACTION100
2.1-2.20.16071500.14542706X-RAY DIFFRACTION100
2.2-2.310.17451570.1532735X-RAY DIFFRACTION100
2.31-2.460.17171520.15472737X-RAY DIFFRACTION100
2.46-2.650.17021410.15662763X-RAY DIFFRACTION100
2.65-2.910.1631510.16012759X-RAY DIFFRACTION100
2.91-3.330.19071380.15662790X-RAY DIFFRACTION100
3.33-4.20.12931190.13542846X-RAY DIFFRACTION100
4.2-29.110.12781630.13612937X-RAY DIFFRACTION100

+
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