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

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Basic information

Entry
Database: PDB / ID: 1epb
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 / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(9cis)-retinoic acid / Epididymal-specific lipocalin-5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 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 16, 2016Group: Non-polymer description
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,1004
Polymers36,5002
Non-polymers6012
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.800, 58.890, 66.650
Angle α, β, γ (deg.)90.00, 109.44, 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 = 258.73 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9954, 0.0363, 0.0886), (0.0398, -0.9985, -0.0387), (0.087, 0.042, -0.9953)
Vector: -2.87, 21.5, 58.07)

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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: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
131 %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: 2.2 Å / Num. obs: 14116 / % possible obs: 94.8 % / Num. measured all: 53778 / Rmerge(I) obs: 0.0688
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.37 Å / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / Rfactor Rwork: 0.182 / Rfactor obs: 0.182 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 44 72 2545
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.37
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: 0.182 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.37

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