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- PDB-1v72: Crystal Structure of Phenylserine Aldolase from Pseudomonas Putida -

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Basic information

Entry
Database: PDB / ID: 1v72
TitleCrystal Structure of Phenylserine Aldolase from Pseudomonas Putida
ComponentsAldolaseFructose-bisphosphate aldolase
KeywordsLYASE / PLP-dependent enzyme
Function / homology
Function and homology information


low-specificity L-threonine aldolase / threonine aldolase activity / threonine catabolic process / metal ion binding
Similarity search - Function
Low specificity L-threonine aldolase, bacteria / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Low specificity L-threonine aldolase, bacteria / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L-threonine aldolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOmi, R.
CitationJournal: To be Published
Title: Crystal Structure of Phenylserine Aldolase from Pseudomonas Putida
Authors: Omi, R. / Miyahara, I. / Misono, H. / Hirotsu, K.
History
DepositionDec 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5413
Polymers38,2281
Non-polymers3132
Water3,711206
1
A: Aldolase
hetero molecules

A: Aldolase
hetero molecules

A: Aldolase
hetero molecules

A: Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,16312
Polymers152,9124
Non-polymers1,2508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area16220 Å2
ΔGint-149 kcal/mol
Surface area44830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.489, 95.489, 107.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Aldolase / Fructose-bisphosphate aldolase


Mass: 38228.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59IT3, EC: 4.1.2.26
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.35 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, PEGMME 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 31555 / Num. obs: 31555 / % possible obs: 99.3 % / Biso Wilson estimate: 16.4 Å2
Reflection shellResolution: 2.05→2.12 Å / % possible all: 99.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.85 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3159 10 %RANDOM
Rwork0.217 ---
obs0.217 31529 99.4 %-
all-31555 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.8036 Å2 / ksol: 0.413087 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 16 206 2802
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.29
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it20.242
X-RAY DIFFRACTIONc_scangle_it16.032.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 510 9.9 %
Rwork0.243 4659 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3param.etctop.plp
X-RAY DIFFRACTION4param.plpintshiff.top
X-RAY DIFFRACTION5ion.paramion.top

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