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- PDB-1epa: STRUCTURE OF THE EPIDIDYMAL RETINOIC ACID-BINDING PROTEIN AT 2.1 ... -

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Basic information

Entry
Database: PDB / ID: 1epa
TitleSTRUCTURE OF THE EPIDIDYMAL RETINOIC ACID-BINDING PROTEIN AT 2.1 ANGSTROMS RESOLUTION
ComponentsEPIDIDYMAL RETINOIC ACID-BINDING PROTEIN
KeywordsRETINOIC ACID-BINDING PROTEIN
Function / homology
Function and homology information


small molecule binding / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Epididymal-specific lipocalin-5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsNewcomer, M.E.
Citation
Journal: Structure / Year: 1993
Title: Structure of the epididymal retinoic acid binding protein at 2.1 A resolution.
Authors: Newcomer, M.E.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: X-Ray Crystallographic Identification of a Protein Binding Site for Both All-Trans-and 9-Cis-Retinoic Acid
Authors: Newcomer, M.E. / Pappas, R.S. / Ong, D.E.
History
DepositionJun 15, 1993Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPIDIDYMAL RETINOIC ACID-BINDING PROTEIN
B: EPIDIDYMAL RETINOIC ACID-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,5002
Polymers36,5002
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.330, 58.670, 66.270
Angle α, β, γ (deg.)90.00, 109.34, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ONLY CA'S ARE GIVEN FOR RESIDUES 24 - 32 IN BOTH COPIES OF THE MOLECULE. ELECTRON DENSITY IN THIS REGION IS POOR.
2: GLY A 72 - PRO A 73 OMEGA = 219.16 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9949, 0.0386, 0.0928), (0.0426, -0.9982, -0.0415), (0.091, 0.0452, -0.9948)
Vector: -2.988, 21.182, 57.79)

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Components

#1: Protein EPIDIDYMAL RETINOIC ACID-BINDING PROTEIN


Mass: 18249.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P06911
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %satammonium sulfate11
210 mMTris-HCl11
310-12 %glycerol11
42.5 mMEDTA11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 16724 / % possible obs: 99.8 % / Num. measured all: 63562 / Rmerge(I) obs: 0.0548
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.26 Å / Mean I/σ(I) obs: 4.8

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→6 Å / Rfactor Rwork: 0.196 / Rfactor obs: 0.196 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 0 119 2549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.73

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