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- PDB-1lrh: Crystal structure of auxin-binding protein 1 in complex with 1-na... -

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Basic information

Entry
Database: PDB / ID: 1lrh
TitleCrystal structure of auxin-binding protein 1 in complex with 1-naphthalene acetic acid
Componentsauxin-binding protein 1
KeywordsPROTEIN BINDING / BETA JELLYROLL / DOUBLE STRANDED PARALLEL BETA HELIX / GERMIN LIKE PROTEIN
Function / homology
Function and homology information


positive regulation of DNA endoreduplication / cytokinesis by cell plate formation / auxin binding / unidimensional cell growth / auxin-activated signaling pathway / positive regulation of cell division / positive regulation of cell size / endoplasmic reticulum lumen / zinc ion binding
Similarity search - Function
Auxin-binding protein / Auxin binding protein / Endoplasmic reticulum targeting sequence. / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NAPHTHALEN-1-YL-ACETIC ACID / Auxin-binding protein 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / difference fourier / Resolution: 1.9 Å
AuthorsWoo, E.J. / Marshall, J. / Bauly, J. / Chen, J.-G. / Venis, M. / Napier, R.M. / Pickersgill, R.W.
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structure of auxin-binding protein 1 in complex with auxin.
Authors: Woo, E.J. / Marshall, J. / Bauly, J. / Chen, J.G. / Venis, M. / Napier, R.M. / Pickersgill, R.W.
History
DepositionMay 15, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_asym_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: auxin-binding protein 1
B: auxin-binding protein 1
C: auxin-binding protein 1
D: auxin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,94616
Polymers73,6474
Non-polymers5,29812
Water6,756375
1
A: auxin-binding protein 1
D: auxin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4738
Polymers36,8242
Non-polymers2,6496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-40 kcal/mol
Surface area13940 Å2
MethodPISA
2
B: auxin-binding protein 1
C: auxin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4738
Polymers36,8242
Non-polymers2,6496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-41 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.583, 82.433, 69.962
Angle α, β, γ (deg.)90.00, 94.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
auxin-binding protein 1


Mass: 18411.809 Da / Num. of mol.: 4 / Mutation: D161E/E162Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ABP1 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P13689
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NLA / NAPHTHALEN-1-YL-ACETIC ACID


Mass: 186.207 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 291 K / pH: 7
Details: Woo, E.J., (2000) Acta Crystallogr., Sect.D, 56, 1476.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1reservoirpH7.0
21 mM1reservoirMgSO4
32 mMsodium azide1reservoir
48.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 54476 / Num. obs: 53495 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.096 / % possible all: 90
Reflection
*PLUS
% possible obs: 94.2 %
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: difference fourier / Resolution: 1.9→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 2714 RANDOM
Rwork0.2 --
all0.2 --
obs0.2 51458 -
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5076 0 348 375 5799
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.0140.02
X-RAY DIFFRACTIONo_angle_d0.0350.04
X-RAY DIFFRACTIONo_planar_d0.0370.05
X-RAY DIFFRACTIONo_chiral_restr0.150.15

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