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- PDB-1bm5: THE SOLUTION STRUCTURE OF A SITE-DIRECTED MUTANT (R111M) OF HUMAN... -

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Basic information

Entry
Database: PDB / ID: 1bm5
TitleTHE SOLUTION STRUCTURE OF A SITE-DIRECTED MUTANT (R111M) OF HUMAN CELLULAR RETIONIC ACID BINDING PROTEIN-TYPE II, NMR, 31 STRUCTURES
ComponentsCELLULAR RETINOIC ACID BINDING PROTEIN-TYPE II
KeywordsRETINOIC-ACID TRANSPORT / CRABPII
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / 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
Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA
AuthorsWang, H. / Yan, H.
CitationJournal: Biochemistry / Year: 1998
Title: NMR study suggests a major role for Arg111 in maintaining the structure and dynamical properties of type II human cellular retinoic acid binding protein.
Authors: Wang, L. / Yan, H.
History
DepositionJul 28, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / 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_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLULAR RETINOIC ACID BINDING PROTEIN-TYPE II


Theoretical massNumber of molelcules
Total (without water)15,5561
Polymers15,5561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 75LEAST RESTRAINT VIOLATION AND LOWEST TOTAL ENERGY
RepresentativeModel #1

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Components

#1: Protein CELLULAR RETINOIC ACID BINDING PROTEIN-TYPE II


Mass: 15555.804 Da / Num. of mol.: 1 / Mutation: R111M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PET-17B / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P29373

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D HOMONUCLEAR
1213D 15N-EDITED NMR EXPERIMENTS

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Sample preparation

DetailsContents: PBS
Sample conditionspH: 7.3 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXR500VarianVXR5005001
Bruker DMX750BrukerDMX7507502

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DGSA / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED FOLLOWING THE STANDARD DISTANCE GEOMETRY-SIMULATED ANNEALING PROTOCAL IN X-PLOR 3.1. SEVERAL ROUNDS OF REFINEMENT WERE PERFORMED.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND LOWEST TOTAL ENERGY
Conformers calculated total number: 75 / Conformers submitted total number: 31

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