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- PDB-4cvw: Structure of the barley limit dextrinase-limit dextrinase inhibit... -

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Basic information

Entry
Database: PDB / ID: 4cvw
TitleStructure of the barley limit dextrinase-limit dextrinase inhibitor complex
Components
  • LIMIT DEXTRINASE
  • LIMIT DEXTRINASE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / STARCH DEBRANCHING ENZYME / GLYCOSIDE HYDROLASE FAMILY 13 / PULLULANASE / CEREAL-TYPE INHIBITOR / CM-PROTEIN / ENDOGENOUS INHIBITOR
Function / homology
Function and homology information


pullulanase activity / polysaccharide catabolic process / serine-type endopeptidase inhibitor activity / extracellular region / metal ion binding
Similarity search - Function
Cereal seed allergen/trypsin and alpha-amylase inhibitor, conserved site / Cereal seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Cereal trypsin/alpha-amylase inhibitors family signature. / 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 / Plant lipid-transfer and hydrophobic proteins ...Cereal seed allergen/trypsin and alpha-amylase inhibitor, conserved site / Cereal seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Cereal trypsin/alpha-amylase inhibitors family signature. / 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 / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Limit dextrinase / Limit dextrinase inhibitor
Similarity search - Component
Biological speciesHORDEUM VULGARE (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsMoeller, M.S. / Vester-Christensen, M.B. / Jensen, J.M. / Abou Hachem, M. / Henriksen, A. / Svensson, B.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of Barley Limit Dextrinase:Limit Dextrinase Inhibitor (Ld:Ldi) Complex Reveals Insights Into Mechanism and Diversity of Cereal-Type Inhibitors.
Authors: Moller, M.S. / Vester-Christensen, M.B. / Jensen, J.M. / Abou Hachem, M. / Henriksen, A. / Svensson, B.
History
DepositionMar 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIMIT DEXTRINASE
B: LIMIT DEXTRINASE
C: LIMIT DEXTRINASE INHIBITOR
D: LIMIT DEXTRINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,0118
Polymers221,8514
Non-polymers1604
Water1,76598
1
A: LIMIT DEXTRINASE
C: LIMIT DEXTRINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0064
Polymers110,9262
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-29.4 kcal/mol
Surface area35430 Å2
MethodPISA
2
B: LIMIT DEXTRINASE
D: LIMIT DEXTRINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0064
Polymers110,9262
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-26.1 kcal/mol
Surface area35400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.979, 168.606, 157.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
22B

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 2 - 23 / Label seq-ID: 1 - 22

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
222BB

NCS ensembles :
ID
1
2

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Components

#1: Protein LIMIT DEXTRINASE


Mass: 97444.156 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-904 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HORDEUM VULGARE (barley) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: O48541, pullulanase
#2: Protein LIMIT DEXTRINASE INHIBITOR


Mass: 13481.414 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HORDEUM VULGARE (barley) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: Q2V8X0
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE VARIATIONS FROM THE ACCESSION NUMBER O48541 ARE AN ARG82LYS SUBSTITUTION AND A ...THE VARIATIONS FROM THE ACCESSION NUMBER O48541 ARE AN ARG82LYS SUBSTITUTION AND A NONE484VAL485THR486-TO- MET484ARG485ALA486 INSERTION-SUBSTITUTION. THE AMINO ACID CHANGES ARE LIKELY TO BE DEPENDENT ON BARLEY CULTIVAR 4 AMINO ACID DISCREPANCIES. THE SEQUENCE STRETCH BETWEEN RESIDUES 484-486 REFLECTS THAT THE CLONED CDNA IS FROM AN OFFSPRING OF THE UNP O48541 SOURCE AND THEREFORE A NATURAL VARIETY

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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: 2.5 Å3/Da / Density % sol: 50.83 % / Description: NONE
Crystal growDetails: PROTEIN STOCK: PURIFIED 1:1 ENZYME:INHIBITOR COMPLEX (A280NM = 12.1) IN 50 MM MES PH 6.6, 250 MM NACL, 0.5 MM CACL2. RESERVOIR: 24% POLYETHYLENE GLYCOL (PEG) 8000 AND 0.05 M KH2PO4. 0.5 ...Details: PROTEIN STOCK: PURIFIED 1:1 ENZYME:INHIBITOR COMPLEX (A280NM = 12.1) IN 50 MM MES PH 6.6, 250 MM NACL, 0.5 MM CACL2. RESERVOIR: 24% POLYETHYLENE GLYCOL (PEG) 8000 AND 0.05 M KH2PO4. 0.5 MICROLITRE 0.1 M NAD WAS ADDED TO THE DROPLET TO A CONCENTRATION OF 0.01 M.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.559
11K, H, -L20.441
ReflectionResolution: 2.67→157.76 Å / Num. obs: 60740 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8
Reflection shellResolution: 2.67→2.85 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2Y4S AND 1B1U

2y4s

1b1u


Resolution: 2.67→157.76 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.847 / SU B: 12.208 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES HAVE BEEN REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3078 5.1 %RANDOM
Rwork0.255 ---
obs0.257 57661 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å20 Å20 Å2
2--10.7 Å20 Å2
3----13.15 Å2
Refinement stepCycle: LAST / Resolution: 2.67→157.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15044 0 4 98 15146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215497
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8471.94820964
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.19451941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79123.717721
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.176152408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.92915112
X-RAY DIFFRACTIONr_chiral_restr0.0550.22278
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111994
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_it0.1671.59687
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.309215585
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.25235732
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4444.55379
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.01 Å

NumberTypeWeight position
88tight positional0.05
85medium positional0.5
88tight thermal0.5
85medium thermal2
LS refinement shellResolution: 2.67→2.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.599 153 -
Rwork0.479 2741 -
obs--62.55 %

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