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- PDB-5hxw: L-amino acid deaminase from Proteus vulgaris -

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Basic information

Entry
Database: PDB / ID: 5hxw
TitleL-amino acid deaminase from Proteus vulgaris
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 / oxidoreductase activity / nucleotide binding / CETYL-TRIMETHYL-AMMONIUM / FLAVIN-ADENINE DINUCLEOTIDE / L-amino acid deaminase
Function and homology information
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 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
DepositionJan 31, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: L-amino acid deaminase
B: L-amino acid deaminase
C: L-amino acid deaminase
D: L-amino acid deaminase
E: L-amino acid deaminase
F: L-amino acid deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,44227
Polymers300,4606
Non-polymers8,98121
Water1,910106
1
A: L-amino acid deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7165
Polymers50,0771
Non-polymers1,6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area18230 Å2
MethodPISA
2
B: L-amino acid deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2857
Polymers50,0771
Non-polymers2,2086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-9 kcal/mol
Surface area18120 Å2
MethodPISA
3
C: L-amino acid deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1473
Polymers50,0771
Non-polymers1,0702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-9 kcal/mol
Surface area17950 Å2
MethodPISA
4
D: L-amino acid deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7165
Polymers50,0771
Non-polymers1,6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-9 kcal/mol
Surface area18030 Å2
MethodPISA
5
E: L-amino acid deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1473
Polymers50,0771
Non-polymers1,0702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area18040 Å2
MethodPISA
6
F: L-amino acid deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4314
Polymers50,0771
Non-polymers1,3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-9 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.314, 104.575, 105.419
Angle α, β, γ (deg.)64.52, 73.06, 61.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
L-amino acid deaminase


Mass: 50076.734 Da / Num. of mol.: 6 / Fragment: UNP residues 30-471
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, L-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-16A / CETYL-TRIMETHYL-AMMONIUM


Mass: 284.543 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C19H42N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 5% m/v PEG 20000, 200mM MES,1mM cetyltrimethylammonium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→94.63 Å / Num. obs: 97176 / % possible obs: 97.2 % / Redundancy: 3.8 % / Net I/σ(I): 31
Reflection shellResolution: 2.63→2.72 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I39

5i39


Resolution: 2.63→94.63 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU B: 31.85 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.825 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25198 4861 5 %RANDOM
Rwork0.22129 ---
obs0.22282 92242 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.747 Å2
Baniso -1Baniso -2Baniso -3
1--3.33 Å2-1.28 Å21.69 Å2
2--1.94 Å20.51 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.63→94.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19615 0 618 106 20339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01920747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.99428251
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.13552591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25124.716844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.786153186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7411597
X-RAY DIFFRACTIONr_chiral_restr0.0720.23141
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115583
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.585.01410355
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0437.52112940
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5895.07610392
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.51342.55730414
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.631→2.699 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 312 -
Rwork0.349 5762 -
obs--82.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4959-0.58180.03612.0454-0.10391.6677-0.1369-0.12360.13520.13750.048-0.0957-0.17580.01120.08890.20560.02470.12350.1323-0.06080.17462.845-2.175-0.086
22.6482-0.567-0.50562.06240.4732.44360.1090.58160.6141-0.4845-0.2127-0.3503-0.36320.1820.10370.31750.06070.14560.42970.26230.2638-33.4037.36443.405
31.947-1.46830.76463.7609-0.90812.11520.23570.2668-0.3732-0.57540.02010.48080.4471-0.2023-0.25580.368-0.1001-0.08880.1137-0.04090.2238-25.43621.046-36.539
44.9671-0.1879-1.69681.4541-0.20832.96130.30070.88470.1607-0.2974-0.31830.4162-0.038-0.69060.01760.07710.1131-0.09550.5589-0.13270.3597-7.775-30.67-34.724
52.9738-0.3262-0.24371.74830.23621.88160.051-0.26540.76140.02490.2078-0.4998-0.34250.832-0.25880.0852-0.22150.06640.6566-0.25340.615-52.948-14.345-10.673
64.9748-0.1353-0.57422.7098-0.05612.6794-0.5077-1.278-0.87740.77550.3020.07330.80970.12460.20570.53510.14270.13190.5290.26280.1694-27.30140.2824.739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 471
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B40 - 471
4X-RAY DIFFRACTION2B501
5X-RAY DIFFRACTION3C42 - 471
6X-RAY DIFFRACTION3C501
7X-RAY DIFFRACTION4D42 - 471
8X-RAY DIFFRACTION4D501
9X-RAY DIFFRACTION5E42 - 471
10X-RAY DIFFRACTION5E501
11X-RAY DIFFRACTION6F42 - 471
12X-RAY DIFFRACTION6F501

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