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- PDB-9wqz: Ala/Ser-specific racemase in complex with PLP-D-Ala -

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Basic information

Entry
Database: PDB / ID: 9wqz
TitleAla/Ser-specific racemase in complex with PLP-D-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
N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE / Alanine/serine racemase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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

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Assembly

Deposited unit
A: Alanine/serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0752
Polymers52,7551
Non-polymers3201
Water1,15364
1
A: Alanine/serine racemase
hetero molecules

A: Alanine/serine racemase
hetero molecules

A: Alanine/serine racemase
hetero molecules

A: Alanine/serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,3018
Polymers211,0204
Non-polymers1,2814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation15_454y-1/2,x+1/2,-z-1/21
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
Buried area26650 Å2
ΔGint-170 kcal/mol
Surface area48480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.793, 100.793, 159.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 52755.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PFC_05380 / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: O58478, Isomerases; Racemases and epimerases; Acting on amino acids and derivatives, alanine racemase
#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: ammonium sulfate, sodium acetate buffer

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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: Mar 8, 2024
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→47.01 Å / Num. obs: 22415 / % possible obs: 100 % / Redundancy: 24.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.033 / Rrim(I) all: 0.164 / Χ2: 0.98 / Net I/σ(I): 19.7
Reflection shellResolution: 2.16→2.23 Å / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 1.659 / Num. measured all: 27012 / Num. unique obs: 1946 / CC1/2: 0.787 / Rpim(I) all: 0.455 / Rrim(I) all: 1.723 / Χ2: 0.97 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→47.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.471 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23813 1073 4.8 %RANDOM
Rwork0.18169 ---
obs0.1844 21339 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.265 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å2-0 Å2-0 Å2
2--2.31 Å2-0 Å2
3----4.61 Å2
Refinement stepCycle: 1 / Resolution: 2.16→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 21 64 3650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163610
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.8344970
X-RAY DIFFRACTIONr_angle_other_deg0.4951.7458339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6415456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.378520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30110645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
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_it2.9033.8391830
X-RAY DIFFRACTIONr_mcbond_other2.9023.8391830
X-RAY DIFFRACTIONr_mcangle_it4.116.8962284
X-RAY DIFFRACTIONr_mcangle_other4.1116.8962285
X-RAY DIFFRACTIONr_scbond_it4.1444.4551838
X-RAY DIFFRACTIONr_scbond_other4.1434.4561838
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5327.9282687
X-RAY DIFFRACTIONr_long_range_B_refined8.04839.94069
X-RAY DIFFRACTIONr_long_range_B_other8.04839.894069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 73 -
Rwork0.31 1547 -
obs--100 %

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