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- PDB-1r43: Crystal structure of beta-alanine synthase from Saccharomyces klu... -

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Basic information

Entry
Database: PDB / ID: 1r43
TitleCrystal structure of beta-alanine synthase from Saccharomyces kluyveri (selenomethionine substituted protein)
Componentsbeta-alanine synthase
KeywordsHYDROLASE / alpha and beta protein / one di-zinc center per subunit
Function / homology
Function and homology information


beta-ureidopropionase activity / beta-ureidopropionase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-AMINO ISOBUTYRATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Beta-alanine synthase
Similarity search - Component
Biological speciesLachancea kluyveri (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsLundgren, S. / Gojkovic, Z. / Piskur, J. / Dobritzsch, D.
Citation
Journal: J.Biol.Chem.
Title: Yeast beta-Alanine Synthase Shares a Structural Scaffold and Origin with Dizinc-dependent Exopeptidases
Authors: Lundgren, S. / Gojkovic, Z. / Piskur, J. / Dobritzsch, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary X-ray analysis of beta-alanine synthase from the yeast Saccharomyces kluyveri
Authors: Dobritzsch, D. / Gojkovic, Z. / Andersen, B. / Piskur, J.
History
DepositionOct 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: beta-alanine synthase
B: beta-alanine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,30610
Polymers102,5642
Non-polymers7428
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-181 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.430, 77.630, 110.570
Angle α, β, γ (deg.)90.00, 95.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNALAALA2AA247 - 364247 - 364
21GLNGLNALAALA2BB247 - 364247 - 364
32LEULEUVALVAL5AA28 - 24628 - 246
42LEULEUVALVAL5BB28 - 24628 - 246
53VALVALHISHIS5AA365 - 455365 - 455
63VALVALHISHIS5BB365 - 455365 - 455
74ZNZNHOHHOH1AC - K500 - 559
84ZNZNHOHHOH1BH - L500 - 1519
DetailsThe biological assembly is a dimer. The asymmetric unit contains one such dimer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein beta-alanine synthase


Mass: 51281.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea kluyveri (fungus) / Gene: PYD3 / Plasmid: P491 / Production host: Escherichia coli (E. coli) / Strain (production host): B843(DE3) / References: UniProt: Q96W94, beta-ureidopropionase

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Non-polymers , 5 types, 76 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-BIB / BETA-AMINO ISOBUTYRATE


Mass: 102.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: trisodium citrate, dioxane, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.0-4.5 mg/mlprotein1drop
250 mMTris1droppH7.5
31 mMdithiothreitol1drop
4100 mM1dropNaCl
51.0 Mtrisodium citrate1reservoir
60.1 MMES1reservoirpH6.5
75 %(v/v)dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793, 0.9794, 0.9393
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 3, 2002 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97941
30.93931
ReflectionResolution: 2.8→30 Å / Num. obs: 25306 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3659 / % possible all: 100
Reflection
*PLUS
Redundancy: 3.8 % / Rmerge(I) obs: 0.119
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.75 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 19.451 / SU ML: 0.371 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27395 1289 5.1 %RANDOM
Rwork0.2106 ---
obs0.21388 23973 99.89 %-
all-23973 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å23.4 Å2
2---3.64 Å20 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6716 0 34 68 6818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216908
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.949349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565868
X-RAY DIFFRACTIONr_chiral_restr0.0870.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025308
X-RAY DIFFRACTIONr_nbd_refined0.2240.23356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.24
X-RAY DIFFRACTIONr_mcbond_it0.291.54306
X-RAY DIFFRACTIONr_mcangle_it0.60426905
X-RAY DIFFRACTIONr_scbond_it1.32432602
X-RAY DIFFRACTIONr_scangle_it2.0314.52444
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
475tight positional0.080.05
1673medium positional0.910.5
1170loose positional1.195
475tight thermal0.10.5
1673medium thermal0.52
1170loose thermal1.3110
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.335 85
Rwork0.3 1810
all-3659
obs-1895
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.2

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