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- PDB-2rhe: STRUCTURE OF A NOVEL BENCE-JONES PROTEIN (RHE) FRAGMENT AT 1.6 AN... -

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Basic information

Entry
Database: PDB / ID: 2rhe
TitleSTRUCTURE OF A NOVEL BENCE-JONES PROTEIN (RHE) FRAGMENT AT 1.6 ANGSTROMS RESOLUTION
ComponentsBENCE-JONES PROTEIN RHE (LIGHT CHAIN)Bence Jones protein
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsFureyjunior, W. / Wang, B.C. / Yoo, C.S. / Sax, M.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Structure of a novel Bence-Jones protein (Rhe) fragment at 1.6 A resolution.
Authors: Furey Jr., W. / Wang, B.C. / Yoo, C.S. / Sax, M.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1979
Title: Phase Extension and Refinement of Bence-Jones Protein Rhe (1.9 Angstroms)
Authors: Fureyjunior, W. / Wang, B.C. / Yoo, C.S. / Sax, M.
#2: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of Bence Jones Protein Rhe (3 Angstroms) and its Unique Domain-Domain Association
Authors: Wang, B.-C. / Yoo, C.S. / Sax, M.
#3: Journal: J.Mol.Biol. / Year: 1974
Title: Structure of a Dimeric Fragment Related to the Lambda-Type Bence-Jones Protein. A Preliminary Study
Authors: Wang, B.-C. / Sax, M.
History
DepositionJun 13, 1983Processing site: BNL
SupersessionSep 15, 1983ID: 1RHE
Revision 1.0Sep 15, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BENCE-JONES PROTEIN RHE (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)11,8411
Polymers11,8411
Non-polymers00
Water3,351186
1
A: BENCE-JONES PROTEIN RHE (LIGHT CHAIN)

A: BENCE-JONES PROTEIN RHE (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)23,6822
Polymers23,6822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)54.630, 52.220, 42.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: SEE REMARK 6. / 2: THE SIDE CHAIN OF RESIDUE ILE 35 IS SLIGHTLY DISORDERED.
DetailsTHIS MOLECULE EXISTS AS A DIMER BOTH IN SOLUTION AND IN THE CRYSTALS, BUT THE TWO-FOLD AXIS OF DIMERIZATION IS ALIGNED WITH THE CRYSTALLOGRAPHIC Z-AXIS. THUS THE ASYMMETRIC UNIT CONTAINS ONLY A MONOMER. TO GENERATE THE INTACT DIMER, APPLY THE OPERATION -X, -Y, Z TO THE COORDINATES BELOW.

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Components

#1: Antibody BENCE-JONES PROTEIN RHE (LIGHT CHAIN) / Bence Jones protein


Mass: 11840.952 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: URINE / References: PIR: S25752
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal grow
*PLUS
pH: 4.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Mphosphate-citrate11
22.0 M11(NH4)2SO4
30.02 %11NaN3

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Data collection

Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 12842 / Observed criterion σ(I): 3 / Rmerge F obs: 0.28 / Num. measured all: 16665

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→10 Å
Details: ALTHOUGH THE CHEMICAL EVIDENCE INDICATES THAT RESIDUE 1 IS PCA (PYROLLIDONE CARBOXYLIC ACID) WHICH IS A CYCLIZED GLUTAMIC ACID, THE COORDINATES GIVEN BELOW ARE THOSE OF THE UNCYCLIZED ...Details: ALTHOUGH THE CHEMICAL EVIDENCE INDICATES THAT RESIDUE 1 IS PCA (PYROLLIDONE CARBOXYLIC ACID) WHICH IS A CYCLIZED GLUTAMIC ACID, THE COORDINATES GIVEN BELOW ARE THOSE OF THE UNCYCLIZED GLUTAMIC ACID (GLU) WHICH WAS USED IN THE REFINEMENT PROCESS. ALMOST NO ELECTRON DENSITY WAS OBSERVED FOR THIS RESIDUE IN THE CRYSTALLOGRAPHIC STUDY INDICATING THAT THIS RESIDUE IS BADLY DISORDERED AND DOES NOT PACK WELL INTO THE LATTICE. THEREFORE NO ATTEMPT WAS MADE TO FIT A PCA GROUP TO THE DATA. THIS DISCREPANCY HAS NO EFFECT ON THE REMAINDER OF THE STRUCTURE. THE SOLVENT STRUCTURE HAS BEEN DETERMINED TO THE EXTENT THAT 35 PER CENT OF ALL WATERS WERE FOUND AND REFINED. THE FIRST 102 WATER SITES ARE FULLY OCCUPIED AND ARE BELIEVED TO BE ACCURATELY PLACED. OCCUPANCIES WERE REFINED FOR THE REMAINING WATER SITES, AND THEIR POSITIONS ARE LIKELY TO BE KNOWN WITH LESS ACCURACY. ALL WATER SITES INCLUDED IN THIS ENTRY ARE CHEMICALLY SENSIBLE IN THAT HYDROGEN BONDS ARE FORMED TO SUITABLE DONORS OR ACCEPTORS AND NO BAD PACKING CONTACTS ARE FORMED. WATERS 115, 117, 118, 121 AND 123 ARE PARTICULARLY SIGNIFICANT AND APPEAR TO BE INTEGRAL PARTS OF THE PROTEIN STRUCTURE.
RfactorNum. reflection
Rwork0.149 -
obs-12763
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 0 186 1019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.024
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Num. reflection obs: 12763 / Rfactor obs: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS

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