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Basic information

Entry
Database: PDB / ID: 1mdc
TitleCRYSTALLIZATION, STRUCTURE DETERMINATION AND LEAST-SQUARES REFINEMENT TO 1.75 ANGSTROMS RESOLUTION OF THE FATTY-ACID-BINDING PROTEIN ISOLATED FROM MANDUCA SEXTA L
ComponentsINSECT FATTY ACID BINDING PROTEIN
KeywordsBINDING PROTEIN
Function / homology
Function and homology information


fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Fatty acid-binding protein 2
Similarity search - Component
Biological speciesManduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsBenning, M. / Holden, H.M.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: Crystallization, structure determination and least-squares refinement to 1.75 A resolution of the fatty-acid-binding protein isolated from Manduca sexta L.
Authors: Benning, M.M. / Smith, A.F. / Wells, M.A. / Holden, H.M.
History
DepositionJul 20, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 6, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A TEN-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A TEN-STRANDED BETA-BARREL. THIS IS REPRESENTED BY AN ELEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INSECT FATTY ACID BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3203
Polymers13,9671
Non-polymers3522
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.500, 70.800, 28.500
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein INSECT FATTY ACID BINDING PROTEIN


Mass: 13967.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm) / References: UniProt: P31417
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, sitting drop / Details: macro-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
111 mg/mlprotein1drop0.02 ml
210 mMHEPES1droppH7.0
31.4 Mammonium sulfate1drop0.02 ml
450 mMNa+-K+ succinate1drop
55 mM1dropNaN3
61.4 Mammonium sulfate1reservoir
750 mMsuccinate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 30 Å / Num. obs: 10674 / % possible obs: 96 % / Num. measured all: 37749

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.75→30 Å / σ(F): 0 /
RfactorNum. reflection
obs0.173 10674
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 23 70 1077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.68
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.68
X-RAY DIFFRACTIONt_dihedral_angle_d18.831
X-RAY DIFFRACTIONt_dihedral_angle_deg

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