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- PDB-1iu9: Crystal structure of the C-terminal domain of aspartate racemase ... -

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Basic information

Entry
Database: PDB / ID: 1iu9
TitleCrystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3
Componentsaspartate racemase
KeywordsISOMERASE / Aspartate racemase / C-terminal domain
Function / homology
Function and homology information


aspartate racemase activity / aspartate racemase
Similarity search - Function
Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsLiu, L. / Iwata, K. / Yohda, M. / Miki, K.
CitationJournal: FEBS LETT. / Year: 2002
Title: Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases
Authors: Liu, L. / Iwata, K. / Yohda, M. / Miki, K.
History
DepositionFeb 28, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2162
Polymers12,1761
Non-polymers401
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.829, 45.328, 57.366
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 aspartate racemase


Mass: 12176.232 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: pPH0670E / Plasmid: pET23c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O58403, aspartate racemase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 37.43 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% Peg8000, 0.10M MES, 0.2M Calcium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.2K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
250 mMTris-HCl1droppH8.0
32 mMmercaptoethanol1drop
416 %PEG80001reservoir
50.10 MMES1reservoirpH6.5
60.20 Mcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2001
RadiationMonochromator: a fixed-exit double crystal monochramator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 34260 / Num. obs: 34023 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.098 / Net I/σ(I): 5.2
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3 / Num. unique all: 837 / Rsym value: 0.226 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 6508 / Num. measured all: 57302
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C-terminal domain in the intact structure of aspartate racemase from Pyrococcus horikoshii OT3

Resolution: 2.04→50 Å / Rfactor Rfree error: 0.015 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 334 5.2 %RANDOM
Rwork0.225 ---
obs0.225 6457 99.4 %-
all-6491 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7606 Å2 / ksol: 0.371495 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2---5.71 Å20 Å2
3---3.8 Å2
Refine analyzeLuzzati coordinate error free: 0.32 Å / Luzzati sigma a free: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 1 56 907
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 60 5.7 %
Rwork0.232 986 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 100 Å / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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