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- PDB-6j35: Crystal structure of ligand-free of PulA-G680L mutant from Klebsi... -

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Basic information

Entry
Database: PDB / ID: 6j35
TitleCrystal structure of ligand-free of PulA-G680L mutant from Klebsiella pneumoniae
ComponentsPullulanase
KeywordsHYDROLASE / Pullulanase / Klebsiella pneumoniae / ligand-free / G680
Function / homology
Function and homology information


pullulanase / pullulanase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Pullulanase, Ins domain / Pullulanase Ins domain / Pullulanase, carbohydrate-binding module 41 / Bacterial pullanase-associated domain / Alpha-1,6-glucosidases, pullulanase-type / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase, N2 domain / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase N2 domain / Rab geranylgeranyltransferase alpha-subunit, insert domain ...Pullulanase, Ins domain / Pullulanase Ins domain / Pullulanase, carbohydrate-binding module 41 / Bacterial pullanase-associated domain / Alpha-1,6-glucosidases, pullulanase-type / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase, N2 domain / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase N2 domain / Rab geranylgeranyltransferase alpha-subunit, insert domain / Immunoglobulin-like - #1110 / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Carbohydrate-binding-like fold / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å
AuthorsSaka, N. / Iwamoto, H. / Takahashi, N. / Mizutani, K. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP16H04909 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Relationship between the induced-fit loop and the activity of Klebsiella pneumoniae pullulanase.
Authors: Saka, N. / Malle, D. / Iwamoto, H. / Takahashi, N. / Mizutani, K. / Mikami, B.
History
DepositionJan 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pullulanase
B: Pullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,48114
Polymers229,0382
Non-polymers44312
Water27,9591552
1
A: Pullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8258
Polymers114,5191
Non-polymers3067
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area37550 Å2
MethodPISA
2
B: Pullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6566
Polymers114,5191
Non-polymers1375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.159, 80.203, 127.301
Angle α, β, γ (deg.)94.92, 103.01, 112.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Pullulanase / PulA protein / Pullulanase-type alpha-1 / 6-glucosidase / DUF3372 domain-containing protein


Mass: 114518.805 Da / Num. of mol.: 2 / Mutation: G680L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: pulA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: W9BQ28
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1552 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN229S was due to spontaneous mutation.

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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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium acetate buffer (pH 6.0), 0.2M magnesium acetate, 20%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.839→50 Å / Num. obs: 181784 / % possible obs: 97.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.037 / Rrim(I) all: 0.06 / Net I/av σ(I): 19.7 / Net I/σ(I): 19.7
Reflection shellResolution: 1.84→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 8.8 / Num. unique obs: 17267 / CC1/2: 0.968 / Rpim(I) all: 0.107 / Rrim(I) all: 0.175 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FHF

2fhf


Resolution: 1.839→38.721 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1895 8226 4.92 %
Rwork0.1642 --
obs0.1654 167203 91.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.839→38.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16056 0 22 1552 17630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116902
X-RAY DIFFRACTIONf_angle_d1.05623087
X-RAY DIFFRACTIONf_dihedral_angle_d21.6616125
X-RAY DIFFRACTIONf_chiral_restr0.082571
X-RAY DIFFRACTIONf_plane_restr0.0073075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8391-1.860.27351510.20662474X-RAY DIFFRACTION42
1.86-1.88190.2481910.18743305X-RAY DIFFRACTION57
1.8819-1.90490.25112200.18293615X-RAY DIFFRACTION63
1.9049-1.9290.23882160.1784050X-RAY DIFFRACTION70
1.929-1.95430.22482180.17144497X-RAY DIFFRACTION76
1.9543-1.98110.23222400.17574735X-RAY DIFFRACTION82
1.9811-2.00940.21822570.16795218X-RAY DIFFRACTION89
2.0094-2.03940.17442520.175398X-RAY DIFFRACTION94
2.0394-2.07130.2282940.17095700X-RAY DIFFRACTION97
2.0713-2.10520.22142910.17475650X-RAY DIFFRACTION97
2.1052-2.14150.2122660.17095701X-RAY DIFFRACTION98
2.1415-2.18050.21052990.17465693X-RAY DIFFRACTION98
2.1805-2.22240.22742800.17435748X-RAY DIFFRACTION98
2.2224-2.26780.2242630.17145618X-RAY DIFFRACTION98
2.2678-2.31710.21282970.17995724X-RAY DIFFRACTION98
2.3171-2.3710.22093220.17025651X-RAY DIFFRACTION98
2.371-2.43020.21062830.17255764X-RAY DIFFRACTION98
2.4302-2.49590.20092980.1755713X-RAY DIFFRACTION98
2.4959-2.56940.19032500.17745686X-RAY DIFFRACTION98
2.5694-2.65230.1892940.17745764X-RAY DIFFRACTION98
2.6523-2.74710.20393180.18015712X-RAY DIFFRACTION98
2.7471-2.8570.2042980.18045760X-RAY DIFFRACTION99
2.857-2.9870.18972900.18535703X-RAY DIFFRACTION98
2.987-3.14440.18492960.17825695X-RAY DIFFRACTION99
3.1444-3.34130.19232960.17765804X-RAY DIFFRACTION99
3.3413-3.59910.16432990.15895667X-RAY DIFFRACTION99
3.5991-3.9610.17882910.14635767X-RAY DIFFRACTION99
3.961-4.53340.14733060.1275770X-RAY DIFFRACTION99
4.5334-5.70870.14443220.13495744X-RAY DIFFRACTION99
5.7087-38.7210.16913280.14855651X-RAY DIFFRACTION98

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