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- PDB-5h06: Crystal structure of AmyP in complex with maltose -

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Basic information

Entry
Database: PDB / ID: 5h06
TitleCrystal structure of AmyP in complex with maltose
ComponentsAmyP
KeywordsHYDROLASE / alpha-amylase / GH13_37
Function / homologyalpha-maltose
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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.type / _entity.formula_weight / _entity.pdbx_description / _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: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _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: AmyP
B: AmyP
C: AmyP
D: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,79816
Polymers282,1084
Non-polymers1,69012
Water39,2192177
1
A: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9494
Polymers70,5271
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint0 kcal/mol
Surface area18910 Å2
MethodPISA
2
B: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9494
Polymers70,5271
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint0 kcal/mol
Surface area18950 Å2
MethodPISA
3
C: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9494
Polymers70,5271
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint2 kcal/mol
Surface area18850 Å2
MethodPISA
4
D: AmyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9494
Polymers70,5271
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint0 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.870, 130.532, 217.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AmyP


Mass: 70527.039 Da / Num. of mol.: 4
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 / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][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 / Water


Mass: 18.015 Da / Num. of mol.: 2177 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl (pH 8.5), 0.2M sodium acetate, 30% (w/v) 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: Jan 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 145235 / % possible obs: 87.6 % / Redundancy: 5 % / Biso Wilson estimate: 13.06 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.053 / Rrim(I) all: 0.122 / Χ2: 1.23 / Net I/av σ(I): 14.184 / Net I/σ(I): 8.8 / Num. measured all: 721686
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.95-2.025.20.4740.878185
2.02-2.14.40.4490.851179.7
2.1-2.25.20.2620.954184.7
2.2-2.314.60.2290.923179
2.31-2.465.20.1510.983185.4
2.46-2.6550.140.984186.4
2.65-2.914.60.1120.972189.2
2.91-3.334.90.0850.992197.3
3.33-4.24.40.0730.99188.7
4.2-4060.0430.998199.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155: ???refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H05

5h05


Resolution: 1.95→39.935 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.79
RfactorNum. reflection% reflection
Rfree0.2123 7292 5.04 %
Rwork0.1635 --
obs0.1659 144717 87.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.76 Å2 / Biso mean: 14.9456 Å2 / Biso min: 2.79 Å2
Refinement stepCycle: final / Resolution: 1.95→39.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15529 0 100 2177 17806
Biso mean--14.97 22.05 -
Num. residues----1990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616020
X-RAY DIFFRACTIONf_angle_d0.82221807
X-RAY DIFFRACTIONf_chiral_restr0.052368
X-RAY DIFFRACTIONf_plane_restr0.0052881
X-RAY DIFFRACTIONf_dihedral_angle_d15.3559441
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 (%)
1.9502-1.97230.33542550.26964328458385
1.9723-1.99550.25122210.17564428464984
1.9955-2.01990.22032380.16434366460485
2.0199-2.04550.25292370.17894416465384
2.0455-2.07240.38812000.31573636383670
2.0724-2.10080.24242190.21554221444081
2.1008-2.13080.20631960.15254454465085
2.1308-2.16260.22142170.15334384460184
2.1626-2.19640.22172350.16544411464685
2.1964-2.23240.23882330.17714424465785
2.2324-2.27090.40862080.28373325353364
2.2709-2.31210.22532410.15314426466785
2.3121-2.35660.21382210.15514439466085
2.3566-2.40470.2152220.14744441466385
2.4047-2.4570.22852310.15364517474886
2.457-2.51410.21792680.1564446471486
2.5141-2.5770.23352590.174480473986
2.577-2.64670.21522460.17944570481687
2.6467-2.72450.26752460.19734344459083
2.7245-2.81240.20362480.15824727497591
2.8124-2.91290.20652420.16844893513593
2.9129-3.02950.18982450.16965062530796
3.0295-3.16730.22542840.17145109539398
3.1673-3.33430.21082980.17455205550399
3.3343-3.5430.20032420.17624700494290
3.543-3.81640.1852430.14955083532695
3.8164-4.20010.17232310.12044316454781
4.2001-4.8070.13762680.108353195587100
4.807-6.05290.15862800.126954105690100
6.0529-39.94340.17383180.15115545586399

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