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- PDB-2zpu: Crystal Structure of Modified Serine Racemase from S.pombe. -

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Basic information

Entry
Database: PDB / ID: 2zpu
TitleCrystal Structure of Modified Serine Racemase from S.pombe.
ComponentsUncharacterized protein C320.14
KeywordsISOMERASE / PLP-dependent / Lyase / Pyridoxal phosphate
Function / homology
Function and homology information


Serine biosynthesis / serine racemase / threonine racemase activity / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / L-serine ammonia-lyase activity / D-serine ammonia-lyase activity / D-serine metabolic process / L-serine metabolic process ...Serine biosynthesis / serine racemase / threonine racemase activity / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / L-serine ammonia-lyase activity / D-serine ammonia-lyase activity / D-serine metabolic process / L-serine metabolic process / pyridoxal phosphate binding / magnesium ion binding / protein homodimerization activity / ATP binding
Similarity search - Function
Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE / Serine racemase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGoto, M.
CitationJournal: J.Biochem. / Year: 2009
Title: Serine racemase with catalytically active lysinoalanyl residue.
Authors: Yamauchi, T. / Goto, M. / Wu, H.Y. / Uo, T. / Yoshimura, T. / Mihara, H. / Kurihara, T. / Miyahara, I. / Hirotsu, K. / Esaki, N.
History
DepositionJul 29, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein C320.14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4383
Polymers35,0931
Non-polymers3452
Water3,387188
1
A: Uncharacterized protein C320.14
hetero molecules

A: Uncharacterized protein C320.14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8756
Polymers70,1862
Non-polymers6894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1740 Å2
ΔGint-15 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.740, 72.990, 65.070
Angle α, β, γ (deg.)90.00, 102.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein C320.14 / Serine Racemase


Mass: 35093.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC320.14, SPCC330.15c / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O59791, serine racemase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PDD / N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE


Type: D-peptide linking / Mass: 320.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% PEG4000, 0.2M Magnesium Acetate, 10% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 29883 / Num. obs: 29440 / % possible obs: 98.9 % / Biso Wilson estimate: 18.4 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VE5

1ve5


Resolution: 1.7→9.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1288548.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2929 10 %RANDOM
Rwork0.183 ---
obs0.183 29360 98.4 %-
all-29883 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.5948 Å2 / ksol: 0.516776 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20.5 Å2
2--0.04 Å20 Å2
3---1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→9.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 22 188 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scbond_it14.722
X-RAY DIFFRACTIONc_scangle_it10.852.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 488 10.4 %
Rwork0.228 4192 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwat.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4plds.paramplds.top
X-RAY DIFFRACTION5int2.paramintshiff2.top

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