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- PDB-5c3u: Crystal structure of a fungal L-serine ammonia-lyase from Rhizomu... -

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Basic information

Entry
Database: PDB / ID: 5c3u
TitleCrystal structure of a fungal L-serine ammonia-lyase from Rhizomucor miehei
ComponentsL-serine ammonia-lyase
KeywordsLYASE / L-serine ammonia-lyase / beta-family PLP dependent enzymes
Function / homology
Function and homology information


threonine deaminase activity / L-serine ammonia-lyase / L-serine ammonia-lyase activity / L-threonine catabolic process / L-serine catabolic process / isoleucine biosynthetic process
Similarity search - Function
: / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L-serine ammonia-lyase
Similarity search - Component
Biological speciesRhizomucor miehei CAU432 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsZhen, Q. / Qiaojuan, Y. / Shaoqing, Y. / Zhengqiang, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure and characterization of a novel l-serine ammonia-lyase from Rhizomucor miehei.
Authors: Qin, Z. / Yan, Q. / Ma, Q. / Jiang, Z.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-serine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6702
Polymers39,4231
Non-polymers2471
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-0 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.980, 72.885, 111.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

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Components

#1: Protein L-serine ammonia-lyase


Mass: 39422.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei CAU432 (fungus) / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0X1KHE6*PLUS, L-serine ammonia-lyase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M KCl, 35% 5/4, PO/OH, and 50 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.76→55.56 Å / Num. obs: 29066 / % possible obs: 97.46 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 45.31
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.49 / % possible all: 91.48

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P5J

1p5j


Resolution: 1.76→55.56 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.413 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20942 1487 5.1 %RANDOM
Rwork0.18635 ---
obs0.18756 27578 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.555 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2--0.12 Å20 Å2
3---1.59 Å2
Refinement stepCycle: 1 / Resolution: 1.76→55.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 15 155 2510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192413
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9663297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4115320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0324.43288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09315388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0091511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211784
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.759→1.804 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 89 -
Rwork0.269 1791 -
obs--91.48 %

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