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- PDB-6lut: Crystal structure of Serine Racemase from Dictyostelium discoideum. -

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Basic information

Entry
Database: PDB / ID: 6lut
TitleCrystal structure of Serine Racemase from Dictyostelium discoideum.
ComponentsProbable serine racemase
KeywordsISOMERASE / D-amino acid / Racemase / PLP
Function / homology
Function and homology information


protein dehydration / Serine metabolism / D-serine biosynthetic process / serine racemase / threonine racemase activity / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase activity ...protein dehydration / Serine metabolism / D-serine biosynthetic process / serine racemase / threonine racemase activity / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase activity / D-serine catabolic process / pyruvate biosynthetic process / L-serine catabolic process / L-serine metabolic process / pyridoxal phosphate binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGoto, M. / Mizobuchi, T. / Yoshimura, T.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2020
Title: Mechanism of eukaryotic serine racemase-catalyzed serine dehydration.
Authors: Ito, T. / Matsuoka, M. / Goto, M. / Watanabe, S. / Mizobuchi, T. / Matsushita, K. / Nasu, R. / Hemmi, H. / Yoshimura, T.
History
DepositionJan 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable serine racemase
B: Probable serine racemase


Theoretical massNumber of molelcules
Total (without water)72,1112
Polymers72,1112
Non-polymers00
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.642, 58.069, 64.530
Angle α, β, γ (deg.)87.400, 72.750, 69.600
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Probable serine racemase / D-serine ammonia-lyase / D-serine dehydratase / L-serine ammonia-lyase / L-serine dehydratase


Mass: 36055.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: srr, DDB_G0289463 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Variant (production host): top10
References: UniProt: Q54HH2, L-serine ammonia-lyase, D-serine ammonia-lyase, serine racemase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 1540, sodium chloride, MPD, PIPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→61.496 Å / Num. all: 109316 / Num. obs: 109316 / % possible obs: 94.4 % / Redundancy: 2.2 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.066 / Rsym value: 0.049 / Net I/av σ(I): 7.2 / Net I/σ(I): 8.7 / Num. measured all: 237696
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.35-1.422.20.3512.233241151950.3190.4760.351290.1
1.42-1.512.20.2133.633006150120.1930.2880.2133.193.6
1.51-1.612.20.1385.531186142240.1250.1870.1384.694.4
1.61-1.742.20.0977.528927132230.0870.1310.0976.394.7
1.74-1.912.20.0689.726666122650.0610.0920.0688.995.2
1.91-2.132.20.0512.424371112240.0450.0670.0512.696.1
2.13-2.462.20.04413.22141299060.0390.0590.0441596.9
2.46-3.022.10.04412.51805784460.0390.0590.04416.797.2
3.02-4.272.10.0413.91384265390.0360.0540.041997.6
4.27-36.7542.10.03714.9698832820.0320.0490.03719.389.6

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.25data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V71

1v71


Resolution: 1.35→36.75 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.661 / SU ML: 0.067 / SU R Cruickshank DPI: 0.0857 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.083 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.268 5411 5 %RANDOM
Rwork0.2478 ---
obs0.2488 103890 94.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.14 Å2 / Biso mean: 19.954 Å2 / Biso min: 11.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.25 Å2-0.64 Å2
2---1.46 Å20.71 Å2
3---0.77 Å2
Refinement stepCycle: final / Resolution: 1.35→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 0 534 5075
Biso mean---30.13 -
Num. residues----611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194623
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9866273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80525.974154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17415813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0581510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213304
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 384 -
Rwork0.334 7063 -
all-7447 -
obs--86.9 %

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