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- PDB-3kdz: X-ray crystal structure of a tyrosine aminomutase mutant construc... -

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Basic information

Entry
Database: PDB / ID: 3kdz
TitleX-ray crystal structure of a tyrosine aminomutase mutant construct with bound ligand
ComponentsHistidine ammonia-lyase
KeywordsLYASE / MIO / AMINOMUTASE / ENEDIYNE / TRANSFERASE / Histidine metabolism
Function / homology
Function and homology information


tyrosine 2,3-aminomutase / tyrosine 2,3-aminomutase activity / tyrosine ammonia-lyase / tyrosine ammonia-lyase activity / toxin biosynthetic process / antibiotic biosynthetic process
Similarity search - Function
Tyrosine 2,3-aminomutase, putative / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal ...Tyrosine 2,3-aminomutase, putative / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TYROSINE / MIO-dependent tyrosine 2,3-aminomutase
Similarity search - Component
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCooke, H.A. / Bruner, S.D.
CitationJournal: Biopolymers / Year: 2010
Title: Probing the active site of MIO-dependent aminomutases, key catalysts in the biosynthesis of beta-amino acids incorporated in secondary metabolites
Authors: Cooke, H.A. / Bruner, S.D.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine ammonia-lyase
B: Histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6684
Polymers116,3062
Non-polymers3622
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-41.4 kcal/mol
Surface area34780 Å2
MethodPISA
2
A: Histidine ammonia-lyase
B: Histidine ammonia-lyase
hetero molecules

A: Histidine ammonia-lyase
B: Histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,3368
Polymers232,6114
Non-polymers7254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area33560 Å2
ΔGint-163.4 kcal/mol
Surface area54820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.722, 145.941, 74.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a head-to-tail homodimer

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Components

#1: Protein Histidine ammonia-lyase /


Mass: 58152.766 Da / Num. of mol.: 2 / Mutation: Y63F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces globisporus (bacteria) / Gene: sgcC4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GMG0, histidine ammonia-lyase
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4.6 M Sodium formate, 95 mM Trimethylamine N-oxide, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 52517 / Num. obs: 50347 / % possible obs: 99.9 % / Redundancy: 14.3 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.087 / Net I/σ(I): 28
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 5174 / % possible all: 100

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OHY

2ohy


Resolution: 2.2→39.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5053 -random
Rwork0.205 ---
all0.23 ---
obs0.205 50153 95.9 %-
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.64 Å20 Å20 Å2
2---12.71 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8024 0 26 216 8266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.305 799 -
Rwork0.27 --
obs-6679 87 %

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