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- PDB-5i39: High resolution structure of L-amino acid deaminase from Proteus ... -

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Basic information

Entry
Database: PDB / ID: 5i39
TitleHigh resolution structure of L-amino acid deaminase from Proteus vulgaris with the deletion of the specific insertion sequence
ComponentsL-amino acid deaminase
KeywordsOXIDOREDUCTASE / membrane protein / l-amino acid oxidase / LAAO / LAD / LAAD
Function / homologyFAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily / nucleotide binding / cytoplasm / FLAVIN-ADENINE DINUCLEOTIDE / L-amino acid deaminase
Function and homology information
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsZhou, H. / Ju, Y. / Niu, L. / Teng, M.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of a membrane-bound l-amino acid deaminase from Proteus vulgaris
Authors: Ju, Y. / Tong, S. / Gao, Y. / Zhao, W. / Liu, Q. / Gu, Q. / Xu, J. / Niu, L. / Teng, M. / Zhou, H.
History
DepositionFeb 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-amino acid deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,15211
Polymers44,8081
Non-polymers1,34410
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.265, 63.708, 125.028
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 L-amino acid deaminase


Mass: 44808.316 Da / Num. of mol.: 1
Fragment: UNP residues 30-471, with deletion of residues 326-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: LAD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LCB2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 285 K / Method: vapor diffusion
Details: 10% PEG 8,000, 0.1 M Hepes pH 7.5, 10% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 139986 / % possible obs: 97.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 34.1
Reflection shellResolution: 1.2→1.24 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15683 6840 4.9 %RANDOM
Rwork0.14083 ---
obs0.14161 132930 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.19 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 89 514 3531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193202
X-RAY DIFFRACTIONr_bond_other_d00.023091
X-RAY DIFFRACTIONr_angle_refined_deg1.372.0064375
X-RAY DIFFRACTIONr_angle_other_deg3.5937147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84724.328134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.71215502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8991521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213610
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02688
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_it0.4931.1891572
X-RAY DIFFRACTIONr_mcbond_other0.4991.2171571
X-RAY DIFFRACTIONr_mcangle_it0.6721.7841972
X-RAY DIFFRACTIONr_mcangle_other0.67214.4021973
X-RAY DIFFRACTIONr_scbond_it0.8291.3331630
X-RAY DIFFRACTIONr_scbond_other0.8291630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.89111.0792383
X-RAY DIFFRACTIONr_long_range_B_refined1.80511.4684197
X-RAY DIFFRACTIONr_long_range_B_other1.80511.4714198
X-RAY DIFFRACTIONr_rigid_bond_restr8.7833202
X-RAY DIFFRACTIONr_sphericity_free16.73596
X-RAY DIFFRACTIONr_sphericity_bonded6.16253539
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 507 -
Rwork0.201 9761 -
obs--98.01 %

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