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- PDB-5h05: Crystal structure of AmyP E221Q in complex with MALTOTRIOSE -

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Basic information

Entry
Database: PDB / ID: 5h05
TitleCrystal structure of AmyP E221Q in complex with MALTOTRIOSE
ComponentsAmyP
KeywordsHYDROLASE / alpha-amylase / GH13_37
Function / homologyalpha-maltotriose
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHe, C. / Liu, Y.
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of a raw-starch-degrading bacterial alpha-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13
Authors: Liu, Y. / Yu, J. / Li, F. / Peng, H. / Zhang, X. / Xiao, Y. / He, C.
History
DepositionOct 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AmyP
B: AmyP
C: AmyP
D: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,44316
Polymers282,1044
Non-polymers2,33812
Water7,764431
1
A: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1114
Polymers70,5261
Non-polymers5853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-18 kcal/mol
Surface area18680 Å2
MethodPISA
2
B: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1114
Polymers70,5261
Non-polymers5853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-18 kcal/mol
Surface area18500 Å2
MethodPISA
3
C: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1114
Polymers70,5261
Non-polymers5853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-19 kcal/mol
Surface area18450 Å2
MethodPISA
4
D: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1114
Polymers70,5261
Non-polymers5853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-19 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.104, 209.894, 113.532
Angle α, β, γ (deg.)90.000, 93.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AmyP


Mass: 70526.055 Da / Num. of mol.: 4 / Mutation: E221Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine metagenome (others) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate (pH 6.0), 22.5% (v/v) 2-propanol, 22.5% (w/v) polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 95440 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.36 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.076 / Rrim(I) all: 0.143 / Χ2: 1.25 / Net I/av σ(I): 11.779 / Net I/σ(I): 6.2 / Num. measured all: 330188
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.55-2.643.50.6420.764199.9
2.64-2.753.50.520.832199.9
2.75-2.873.50.3860.892199.9
2.87-3.023.50.2910.934199.9
3.02-3.213.50.2250.9571100
3.21-3.463.50.1610.976199.8
3.46-3.813.40.1080.987199.7
3.81-4.363.40.0820.991199.4
4.36-5.493.40.0590.995199.5
5.49-403.50.0480.997199.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155: ???refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J0H

1j0h


Resolution: 2.55→37.577 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.69
RfactorNum. reflection% reflection
Rfree0.22 4716 4.95 %
Rwork0.1702 --
obs0.1726 95368 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.72 Å2 / Biso mean: 37.1045 Å2 / Biso min: 15.58 Å2
Refinement stepCycle: final / Resolution: 2.55→37.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15468 0 144 431 16043
Biso mean--34.88 36.35 -
Num. residues----1983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816015
X-RAY DIFFRACTIONf_angle_d0.93321810
X-RAY DIFFRACTIONf_chiral_restr0.0522382
X-RAY DIFFRACTIONf_plane_restr0.0052872
X-RAY DIFFRACTIONf_dihedral_angle_d18.0949364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5484-2.57740.3591520.2882844299694
2.5774-2.60770.3571550.271830233178100
2.6077-2.63950.31851600.267130863246100
2.6395-2.67290.33291570.262229253082100
2.6729-2.70810.32021540.257630673221100
2.7081-2.74520.31311750.248430373212100
2.7452-2.78440.27251520.222429803132100
2.7844-2.82590.27481470.208830593206100
2.8259-2.87010.26581450.220230623207100
2.8701-2.91710.26661630.212129993162100
2.9171-2.96740.28591540.202930303184100
2.9674-3.02130.23781770.196330273204100
3.0213-3.07940.27181390.192630153154100
3.0794-3.14220.24311630.195730533216100
3.1422-3.21050.26271580.192629773135100
3.2105-3.28510.24511630.181930483211100
3.2851-3.36720.25411470.181730653212100
3.3672-3.45820.24591550.184730223177100
3.4582-3.55990.22421780.168129883166100
3.5599-3.67470.2061420.154130673209100
3.6747-3.80590.18011540.144330123166100
3.8059-3.95820.191610.14373050321199
3.9582-4.13810.19581460.13962998314499
4.1381-4.3560.21381240.128530553179100
4.356-4.62840.13521670.12053000316799
4.6284-4.9850.15961690.120930393208100
4.985-5.48530.16981580.12830253183100
5.4853-6.27590.17751750.148330633238100
6.2759-7.89490.1811700.158430193189100
7.8949-37.58150.19131560.15763017317398

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