[English] 日本語
Yorodumi
- PDB-5yyc: Crystal structure of alanine racemase from Bacillus pseudofirmus (OF4) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yyc
TitleCrystal structure of alanine racemase from Bacillus pseudofirmus (OF4)
ComponentsAlanine racemase
KeywordsISOMERASE / Alanine racemase / Bacillus pseudofirmus (OF4)
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding
Similarity search - Function
Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Alanine racemase
Similarity search - Component
Biological speciesBacillus pseudofirmus
MethodX-RAY DIFFRACTION / Resolution: 1.801 Å
AuthorsDong, H. / Hu, T.T. / He, G.Z. / Lu, D.R. / Qi, J.X. / Dou, Y.S. / Long, W. / He, X. / Su, D. / Ju, J.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China30970628 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural features and kinetic characterization of alanine racemase from Bacillus pseudofirmus OF4.
Authors: Dong, H. / Hu, T. / He, G. / Lu, D. / Qi, J. / Dou, Y. / Long, W. / He, X. / Ju, J. / Su, D.
History
DepositionDec 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alanine racemase
C: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2344
Polymers80,7402
Non-polymers4942
Water16,087893
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-11 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.301, 97.314, 112.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Alanine racemase /


Mass: 40369.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pseudofirmus (strain OF4) (bacteria)
Strain: OF4 / Gene: alr, BpOF4_09770 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: D3FSP1, alanine racemase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.4M sodium/potassium phosphate pH 8.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 99024 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.058 / Χ2: 1.413 / Net I/σ(I): 35.796
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.586 / Χ2: 1.278

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementResolution: 1.801→21.766 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 5003 5.06 %5
Rwork0.1492 ---
obs0.1505 98915 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→21.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 30 893 6565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085780
X-RAY DIFFRACTIONf_angle_d1.0677828
X-RAY DIFFRACTIONf_dihedral_angle_d13.7392116
X-RAY DIFFRACTIONf_chiral_restr0.046904
X-RAY DIFFRACTIONf_plane_restr0.0051008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8007-1.82120.26121630.23232867X-RAY DIFFRACTION94
1.8212-1.84260.27491590.21393166X-RAY DIFFRACTION100
1.8426-1.86510.21761490.19273080X-RAY DIFFRACTION100
1.8651-1.88860.22031340.18113132X-RAY DIFFRACTION100
1.8886-1.91350.20651800.16463115X-RAY DIFFRACTION100
1.9135-1.93970.18551820.1653078X-RAY DIFFRACTION100
1.9397-1.96740.18351580.15793086X-RAY DIFFRACTION100
1.9674-1.99670.18491450.15563155X-RAY DIFFRACTION100
1.9967-2.02790.16191710.15783106X-RAY DIFFRACTION100
2.0279-2.06110.16781790.15873075X-RAY DIFFRACTION100
2.0611-2.09660.1551440.15263124X-RAY DIFFRACTION100
2.0966-2.13470.15511460.13733108X-RAY DIFFRACTION100
2.1347-2.17580.16981880.1483073X-RAY DIFFRACTION100
2.1758-2.22010.15541620.14893201X-RAY DIFFRACTION100
2.2201-2.26830.18842170.15393038X-RAY DIFFRACTION100
2.2683-2.32110.18361810.14443088X-RAY DIFFRACTION100
2.3211-2.3790.17471550.15693129X-RAY DIFFRACTION100
2.379-2.44330.19961560.15233159X-RAY DIFFRACTION100
2.4433-2.51510.17471770.15433081X-RAY DIFFRACTION100
2.5151-2.59610.18861770.14963139X-RAY DIFFRACTION100
2.5961-2.68870.13861870.14433135X-RAY DIFFRACTION100
2.6887-2.79620.1551740.13673135X-RAY DIFFRACTION100
2.7962-2.92320.1861440.14763155X-RAY DIFFRACTION100
2.9232-3.07690.15531530.14233151X-RAY DIFFRACTION100
3.0769-3.26910.16121630.13473192X-RAY DIFFRACTION100
3.2691-3.52050.15561920.12643147X-RAY DIFFRACTION100
3.5205-3.8730.14381750.11853177X-RAY DIFFRACTION100
3.873-4.42930.14851620.1273217X-RAY DIFFRACTION100
4.4293-5.5650.18631480.15043251X-RAY DIFFRACTION100
5.565-21.76730.23481820.2043352X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -6.1296 Å / Origin y: 30.357 Å / Origin z: -14.1296 Å
111213212223313233
T0.1606 Å20.0172 Å20.0149 Å2-0.1604 Å20.0143 Å2--0.1715 Å2
L0.3572 °20.168 °20.1891 °2-0.359 °20.1909 °2--0.49 °2
S-0.0078 Å °-0.0082 Å °-0.0052 Å °-0.0086 Å °-0.0084 Å °-0.0052 Å °-0.0067 Å °-0.0095 Å °0.0213 Å °
Refinement TLS groupSelection details: all

+
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