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- PDB-1rj4: Structure of a Cell Wall Invertase Inhibitor from Tobacco in Comp... -

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Basic information

Entry
Database: PDB / ID: 1rj4
TitleStructure of a Cell Wall Invertase Inhibitor from Tobacco in Complex with Cd2+
Componentsinvertase inhibitor
KeywordsPROTEIN BINDING / FOUR-HELIX BUNDLE / HELICAL HAIRPIN / CADMIUM COORDINATION / BIS-TRIS BUFFER
Function / homology
Function and homology information


plant-type cell wall modification / plant-type cell wall / enzyme inhibitor activity / hydrolase activity
Similarity search - Function
Cell wall/vacuolar inhibitor of fructosidase / Invertase/pectin methylesterase inhibitor family protein / Pectinesterase inhibitor domain / Invertase/pectin methylesterase inhibitor domain superfamily / Plant invertase/pectin methylesterase inhibitor / Plant invertase/pectin methylesterase inhibitor / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Cell wall / vacuolar inhibitor of fructosidase 1
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsHothorn, M. / D'Angelo, I. / Marquez, J.A. / Greiner, S. / Scheffzek, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The invertase inhibitor Nt-CIF from tobacco: a highly thermostable four-helix bundle with an unusual N-terminal extension
Authors: Hothorn, M. / D'Angelo, I. / Marquez, J.A. / Greiner, S. / Scheffzek, K.
History
DepositionNov 18, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: invertase inhibitor
B: invertase inhibitor
C: invertase inhibitor
D: invertase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,09016
Polymers64,3544
Non-polymers1,73612
Water4,252236
1
A: invertase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5234
Polymers16,0881
Non-polymers4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: invertase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5234
Polymers16,0881
Non-polymers4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: invertase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5234
Polymers16,0881
Non-polymers4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: invertase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5234
Polymers16,0881
Non-polymers4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.170, 95.639, 126.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer in solution

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Components

#1: Protein
invertase inhibitor


Mass: 16088.454 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Tissue: cell wall / Gene: NTINH1 / Plasmid: pETM20 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: O49908
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.72 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.0M sodium formate, 0.1M bis-Tris buffer, 0.03 M CDCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Hothorn, M., (2003) Acta Cryst., D59, 2279.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
24 Msodium formate1reservoir
30.1 MBis-Tris1reservoirpH7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→19.67 Å / Num. all: 49180 / Num. obs: 49162 / % possible obs: 1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 16.09
Reflection shellResolution: 2→2.15 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 7.72 / Num. unique all: 9425 / Rsym value: 0.258 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 49059 / % possible obs: 100 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 9428 / Rmerge(I) obs: 0.258

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2→19.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2195351.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2455 5 %RANDOM
Rwork0.212 ---
obs0.212 49095 100 %-
all-49095 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1757 Å2 / ksol: 0.38682 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---6.18 Å20 Å2
3---7.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 64 236 4692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 404 5 %
Rwork0.235 7675 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Num. reflection obs: 49059
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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