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- PDB-5fjm: Structure of L-Amino acid deaminase from Proteus myxofaciens -

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Basic information

Entry
Database: PDB / ID: 5fjm
TitleStructure of L-Amino acid deaminase from Proteus myxofaciens
ComponentsL-AMINO ACID DEAMINASE
KeywordsHYDROLASE / L-AMINO ACID DEAMINASE / FLAVOPROTEIN / FLAVOENZYME / MEMBRANE PROTEIN
Function / homology
Function and homology information


D-amino-acid dehydrogenase activity / D-alanine catabolic process / nucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / L-amino acid deaminase
Similarity search - Component
Biological speciesPROTEUS MYXOFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMotta, P. / Molla, G. / Pollegioni, L. / Nardini, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure-Function Relationships in L-Amino Acid Deaminase, a Flavoprotein Belonging to a Novel Class of Biotechnologically Relevant Enzymes
Authors: Motta, P. / Molla, G. / Pollegioni, L. / Nardini, M.
History
DepositionOct 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: L-AMINO ACID DEAMINASE
B: L-AMINO ACID DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6624
Polymers100,0912
Non-polymers1,5712
Water9,314517
1
A: L-AMINO ACID DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8312
Polymers50,0461
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-AMINO ACID DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8312
Polymers50,0461
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.760, 93.710, 74.690
Angle α, β, γ (deg.)90.00, 102.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein L-AMINO ACID DEAMINASE


Mass: 50045.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROTEUS MYXOFACIENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A158RFS7*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.48 Å3/Da / Density % sol: 50.49 % / Description: NONE
Crystal growpH: 6.5 / Details: 15% PEG 6K, 0.1 M MES (PH 6.5), 10% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87257
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87257 Å / Relative weight: 1
ReflectionResolution: 2→49.08 Å / Num. obs: 65982 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GAG

2gag


Resolution: 2→46.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.779 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY POOR ELECTRON DENSITY IS PRESENT AT THE N- AND C-TERMINUS (RESIDUES 28 AND 474 OF BOTH A AND B CHAINS)
RfactorNum. reflection% reflectionSelection details
Rfree0.20898 3340 5.1 %RANDOM
Rwork0.17691 ---
obs0.17855 62619 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.967 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.04 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 106 517 7511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197181
X-RAY DIFFRACTIONr_bond_other_d0.0010.026826
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9799761
X-RAY DIFFRACTIONr_angle_other_deg0.73315754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19523.933300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.034151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3691547
X-RAY DIFFRACTIONr_chiral_restr0.0620.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021583
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_it1.0012.5043584
X-RAY DIFFRACTIONr_mcbond_other1.0012.5023583
X-RAY DIFFRACTIONr_mcangle_it1.7543.7464479
X-RAY DIFFRACTIONr_mcangle_other1.7543.7484480
X-RAY DIFFRACTIONr_scbond_it1.0162.6273597
X-RAY DIFFRACTIONr_scbond_other1.0162.6273598
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7643.8685278
X-RAY DIFFRACTIONr_long_range_B_refined3.80520.1728568
X-RAY DIFFRACTIONr_long_range_B_other3.71220.0948481
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 238 -
Rwork0.245 4593 -
obs--99.9 %

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