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- PDB-9wu1: Amino acid racemase in complex with PLP-D-Phe -

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Basic information

Entry
Database: PDB / ID: 9wu1
TitleAmino acid racemase in complex with PLP-D-Phe
ComponentsBroad substrate specificity amino-acid racemase
KeywordsISOMERASE / racemase / fold type 1
Function / homology
Function and homology information


methionine racemase activity / amino-acid racemase / threonine racemase activity / transaminase activity / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
: / 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
: / Broad substrate specificity amino-acid racemase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Broad substrate specificity amino-acid racemase
B: Broad substrate specificity amino-acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4274
Polymers108,6342
Non-polymers7932
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-96 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.901, 133.203, 135.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Broad substrate specificity amino-acid racemase / BAR


Mass: 54317.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0138 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O57878, amino-acid racemase
#2: Chemical ChemComp-A1MB8 / (2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-phenyl-propanoic acid


Type: D-peptide linking / Mass: 396.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 3-methyl-1,5-pentanediol, sodium acetate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 19, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.5 Å / Num. obs: 68318 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.99 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 4551 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.51 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.112 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19976 3398 5 %RANDOM
Rwork0.16809 ---
obs0.16975 64838 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.874 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å2-0 Å20 Å2
2--1.35 Å2-0 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 0 54 250 7584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167248
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.65110161
X-RAY DIFFRACTIONr_angle_other_deg1.3471.58916759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3365918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81822.419372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1531544
X-RAY DIFFRACTIONr_chiral_restr0.1090.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021626
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_it3.1113.9923681
X-RAY DIFFRACTIONr_mcbond_other3.1113.9923680
X-RAY DIFFRACTIONr_mcangle_it4.1375.984596
X-RAY DIFFRACTIONr_mcangle_other4.1365.984597
X-RAY DIFFRACTIONr_scbond_it4.4054.5333828
X-RAY DIFFRACTIONr_scbond_other4.4054.5333829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5676.5925566
X-RAY DIFFRACTIONr_long_range_B_refined7.82847.6938593
X-RAY DIFFRACTIONr_long_range_B_other7.82947.6588574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 249 -
Rwork0.288 4727 -
obs--99.86 %

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