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- PDB-3vm5: Recombinant medaka fish alpha-amylase expressed in yeast Pichia p... -

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Basic information

Entry
Database: PDB / ID: 3vm5
TitleRecombinant medaka fish alpha-amylase expressed in yeast Pichia pastoris
Componentsalpha-amylase
KeywordsHYDROLASE / (alpha/beta)8 barrel fold / starch hydrolysis
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular space / metal ion binding
Similarity search - Function
Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryzias latipes (Japanese medaka)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMizutani, K. / Toyoda, M. / Mikami, B.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Structural and functional characterization of recombinant medaka fish alpha-amylase expressed in yeast Pichia pastoris.
Authors: Mizutani, K. / Toyoda, M. / Otake, Y. / Yoshioka, S. / Takahashi, N. / Mikami, B.
History
DepositionDec 8, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7863
Polymers56,7111
Non-polymers762
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.045, 83.045, 174.228
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein alpha-amylase


Mass: 56710.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Strain: Hd-rR / Plasmid: p9KPrAHS / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71 / References: UniProt: H2N0D4*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 22.5% PEG 3350, 0.2M sodium nitrate, 50mM Tris-HCl, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 21, 2011
RadiationMonochromator: rhodium-coated mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 17095 / Num. obs: 17061 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 32.9
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 8 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 6.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Rayonixdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PIF

1pif


Resolution: 2.85→27.73 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 807 5.04 %5
Rwork0.1768 ---
all0.177 17095 --
obs0.1803 15999 94.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 3.951 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2081 Å20 Å20 Å2
2---1.2081 Å20 Å2
3---2.4161 Å2
Refinement stepCycle: LAST / Resolution: 2.85→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 2 47 3987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094060
X-RAY DIFFRACTIONf_angle_d1.1555506
X-RAY DIFFRACTIONf_dihedral_angle_d22.092436
X-RAY DIFFRACTIONf_chiral_restr0.082539
X-RAY DIFFRACTIONf_plane_restr0.005740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8504-3.02870.35281280.2517230189
3.0287-3.26230.30821390.2206241192
3.2623-3.58990.28211380.1948249995
3.5899-4.1080.24931380.1574253496
4.108-5.17010.18551390.143263998
5.1701-27.73170.21981250.1686280899

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