[English] 日本語
Yorodumi
- PDB-8hpg: Crystal structure of phenylpyruvate reductase from Lactobacillus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hpg
TitleCrystal structure of phenylpyruvate reductase from Lactobacillus sp. CGMCC 9967
ComponentsPhenylpyruvate reductase
KeywordsOXIDOREDUCTASE / phenylpyruvate reductase
Function / homologyphosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD binding / NAD(P)-binding domain superfamily / Phenylpyruvate reductase
Function and homology information
Biological speciesLactobacillus sp. CGMCC 9967 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.895 Å
AuthorsYang, J.H. / Song, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: One-Pot Biocatalytic Transformation of L-DOPA to D-Danshensu
Authors: Yang, J.H. / Song, W.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylpyruvate reductase
B: Phenylpyruvate reductase


Theoretical massNumber of molelcules
Total (without water)67,5052
Polymers67,5052
Non-polymers00
Water00
1
A: Phenylpyruvate reductase


Theoretical massNumber of molelcules
Total (without water)33,7531
Polymers33,7531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenylpyruvate reductase


Theoretical massNumber of molelcules
Total (without water)33,7531
Polymers33,7531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.896, 48.970, 89.896
Angle α, β, γ (deg.)90.00, 116.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phenylpyruvate reductase


Mass: 33752.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. CGMCC 9967 (bacteria)
Gene: ppr / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M5IHP7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 3.5
Details: PEG 1000, Citric acid, B-Nicotinamide adeinie dinucleotide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54184 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3.89→23.49 Å / Num. obs: 3064 / % possible obs: 86.7394 % / Redundancy: 2 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.062 / Net I/σ(I): 7.29
Reflection shellResolution: 3.89→4.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.371 / Num. unique obs: 925 / CC1/2: 0.748 / % possible all: 54.7

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5refinement
HKL-2000data reduction
SHELXCDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.895→23.49 Å / Cor.coef. Fo:Fc: 0.664 / Cor.coef. Fo:Fc free: 0.605 / SU B: 8.898 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 141 4.6 %RANDOM
Rwork0.25755 ---
obs0.25875 2909 86.7394 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.129 Å2
Baniso -1Baniso -2Baniso -3
1--87.97 Å2-0 Å225.56 Å2
2--131.05 Å20 Å2
3----43.08 Å2
Refinement stepCycle: 1 / Resolution: 3.895→23.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 0 0 4680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134776
X-RAY DIFFRACTIONr_bond_other_d0.0040.0154637
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6356499
X-RAY DIFFRACTIONr_angle_other_deg1.0161.57610655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.645612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12322.613222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59915781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5921526
X-RAY DIFFRACTIONr_chiral_restr0.0460.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025414
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021042
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3514.62460
X-RAY DIFFRACTIONr_mcbond_other4.354.5992458
X-RAY DIFFRACTIONr_mcangle_it6.0936.8693068
X-RAY DIFFRACTIONr_mcangle_other6.0916.8683068
X-RAY DIFFRACTIONr_scbond_it3.2214.6322316
X-RAY DIFFRACTIONr_scbond_other3.2214.6322317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6496.9743432
X-RAY DIFFRACTIONr_long_range_B_refined7.97451.9095072
X-RAY DIFFRACTIONr_long_range_B_other7.97451.9125073
X-RAY DIFFRACTIONr_rigid_bond_restr1.97639413
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8966 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.895→3.895 Å
RfactorNum. reflection% reflection
Rfree0 20 -
Rwork0 6139 -
obs--21 %

+
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