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- PDB-9wr1: Ala/Ser-specific racemase in complex with PLP-L-Ala -

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Basic information

Entry
Database: PDB / ID: 9wr1
TitleAla/Ser-specific racemase in complex with PLP-L-Ala
ComponentsAlanine/serine racemase
KeywordsISOMERASE / fold type 1 / racemase
Function / homology
Function and homology information


serine racemase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / alanine racemase / alanine racemase activity / transaminase activity / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
: / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
ALANYL-PYRIDOXAL-5'-PHOSPHATE / Alanine/serine racemase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSakuraba, H. / Yoneda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Crystal structures of two different 4-aminobutyrate aminotransferase-like racemases from the hyperthermophilic archaeon Pyrococcus horikoshii.
Authors: Kawakami, R. / Nishimoto, Y. / Kawase, T. / Hayashi, J. / Yoneda, K. / Ohshima, T. / Sakuraba, H.
History
DepositionSep 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alanine/serine racemase
B: Alanine/serine racemase
C: Alanine/serine racemase
D: Alanine/serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,3018
Polymers211,0204
Non-polymers1,2814
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26480 Å2
ΔGint-163 kcal/mol
Surface area51460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.184, 150.203, 104.085
Angle α, β, γ (deg.)90.00, 100.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alanine/serine racemase / ASR / Ala/Ser racemase


Mass: 52755.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0782 / Production host: Escherichia coli (E. coli)
References: UniProt: O58478, Isomerases; Racemases and epimerases; Acting on amino acids and derivatives, alanine racemase
#2: Chemical
ChemComp-PP3 / ALANYL-PYRIDOXAL-5'-PHOSPHATE / PYRIDOXYL-ALANINE-5-PHOSPHATE / VITAMIN B6 COMPLEXED WITH ALANINE


Mass: 320.236 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG400, HEPES buffer, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.46 Å / Num. obs: 68557 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.073 / Rrim(I) all: 0.193 / Χ2: 0.97 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.46 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.062 / Num. measured all: 32469 / Num. unique obs: 4594 / CC1/2: 0.824 / Rpim(I) all: 0.428 / Rrim(I) all: 1.146 / Χ2: 0.99 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.46 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.155 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R: 0.768 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25962 3415 5 %RANDOM
Rwork0.20964 ---
obs0.21215 65105 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.26 Å2
Baniso -1Baniso -2Baniso -3
1-8.67 Å2-0 Å22.52 Å2
2---5.48 Å2-0 Å2
3----3.87 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14286 0 84 272 14642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01214700
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614455
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.83419918
X-RAY DIFFRACTIONr_angle_other_deg0.4751.74533388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71351828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.408581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.047102579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.22222
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023134
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_it2.6634.1897336
X-RAY DIFFRACTIONr_mcbond_other2.6634.1897336
X-RAY DIFFRACTIONr_mcangle_it4.2217.5259156
X-RAY DIFFRACTIONr_mcangle_other4.2217.5259157
X-RAY DIFFRACTIONr_scbond_it2.9564.5917364
X-RAY DIFFRACTIONr_scbond_other2.9564.5917360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9458.28910757
X-RAY DIFFRACTIONr_long_range_B_refined7.06642.0516492
X-RAY DIFFRACTIONr_long_range_B_other7.06642.0516478
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 264 -
Rwork0.338 4777 -
obs--100 %

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