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- PDB-1acd: V32D/F57H MUTANT OF MURINE ADIPOCYTE LIPID BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1acd
TitleV32D/F57H MUTANT OF MURINE ADIPOCYTE LIPID BINDING PROTEIN
ComponentsADIPOCYTE LIPID BINDING PROTEIN
KeywordsFATTY ACID BINDING PROTEIN
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / cholesterol homeostasis ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / cholesterol homeostasis / fatty acid binding / fatty acid metabolic process / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / nucleoplasm / nucleus / cytosol / cytoplasm
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
Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOry, J. / Kane, C.D. / Simpson, M. / Banaszak, L.J. / Bernlohr, D.A.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Biochemical and crystallographic analyses of a portal mutant of the adipocyte lipid-binding protein.
Authors: Ory, J. / Kane, C.D. / Simpson, M.A. / Banaszak, L.J. / Bernlohr, D.A.
History
DepositionFeb 6, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 16, 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: ADIPOCYTE LIPID BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,5331
Polymers14,5331
Non-polymers00
Water00
1
A: ADIPOCYTE LIPID BINDING PROTEIN

A: ADIPOCYTE LIPID BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,0652
Polymers29,0652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_653-x+1,y,-z-3/21
Unit cell
Length a, b, c (Å)79.490, 97.290, 50.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ADIPOCYTE LIPID BINDING PROTEIN / ALBP


Mass: 14532.526 Da / Num. of mol.: 1 / Mutation: C1G, V32D, F57H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: ADIPOCYTE / Production host: Escherichia coli (E. coli) / References: UniProt: P04117
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: 3.4 Å3/Da / Density % sol: 64.4 %
Crystal growpH: 6.4 / Details: 2.4M PHOSPHATE, PH 6.4
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112.5 mMHEPES1reservoir
210 mg/mlprotein1reservoir
32.4 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 22, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 26696 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 54.2 Å2 / Rsym value: 0.096 / Net I/σ(I): 10.4
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.99 / Rsym value: 0.419 / % possible all: 57.3
Reflection
*PLUS
Num. measured all: 54873 / Rmerge(I) obs: 0.1313

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIB

1lib


Resolution: 2.7→30 Å / Rfactor Rfree error: 0.0004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 514 10.1 %RANDOM
Rwork0.198 ---
obs0.198 4452 78.8 %-
Displacement parametersBiso mean: 27.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.574 Å0.41 Å
Luzzati d res low-30 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 0 0 1017
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.325 19 2.76 %
Rwork0.324 145 -
obs--23.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2CYO.PARAMCYO.TOPPAR
Software
*PLUS
Name: X-PLOR / Version: 3.843C / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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