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- PDB-6rlx: X-RAY STRUCTURE OF HUMAN RELAXIN AT 1.5 ANGSTROMS. COMPARISON TO ... -

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Basic information

Entry
Database: PDB / ID: 6rlx
TitleX-RAY STRUCTURE OF HUMAN RELAXIN AT 1.5 ANGSTROMS. COMPARISON TO INSULIN AND IMPLICATIONS FOR RECEPTOR BINDING DETERMINANTS
Components
  • RELAXIN, A-CHAIN
  • RELAXIN, B-CHAIN
KeywordsHORMONE(MUSCLE RELAXANT)
Function / homology
Function and homology information


Relaxin receptors / regulation of catalytic activity / female pregnancy / hormone activity / positive regulation of angiogenesis / G alpha (s) signalling events / positive regulation of gene expression / extracellular region
Similarity search - Function
Relaxin / : / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsEigenbrot, C. / Randal, M. / Kossiakoff, A.A.
CitationJournal: J.Mol.Biol. / Year: 1991
Title: X-ray structure of human relaxin at 1.5 A. Comparison to insulin and implications for receptor binding determinants.
Authors: Eigenbrot, C. / Randal, M. / Quan, C. / Burnier, J. / O'Connell, L. / Rinderknecht, E. / Kossiakoff, A.A.
History
DepositionJun 21, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RELAXIN, A-CHAIN
B: RELAXIN, B-CHAIN
C: RELAXIN, A-CHAIN
D: RELAXIN, B-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,7244
Polymers11,7244
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-41 kcal/mol
Surface area5620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.970, 56.880, 61.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: WATERS 402, 404, 508, 509, AND 542 SHARE SOME DISTANCES TOO SHORT FOR INDEPENDENT MOLECULES. THEY MAY REPRESENT AN INCOMPLETELY RESOLVED CITRATE ION. FOR WATERS 403, 442, 502, 510, AND 541, THE ...1: WATERS 402, 404, 508, 509, AND 542 SHARE SOME DISTANCES TOO SHORT FOR INDEPENDENT MOLECULES. THEY MAY REPRESENT AN INCOMPLETELY RESOLVED CITRATE ION. FOR WATERS 403, 442, 502, 510, AND 541, THE SAME APPLIES. THESE PSEUDO-TWO-FOLD RELATED CLUSTERS ARE FOUND NEAR THE N-TERMINI OF THE A-CHAINS.
Components on special symmetry positions
IDModelComponents
11C-71-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.830125, 0.207228, -0.517638), (0.164367, -0.978064, -0.127962), (-0.532801, 0.021142, -0.845977)
Vector: 19.36984, 28.26602, 77.56604)
DetailsPSEUDO TWO-FOLD CALCULATED FROM C ALPHA PORTIONS A 6 - A 20 AND B 7 - B 19 AND THE CORRESPONDING ATOMS OF MOLECULE 2. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *C* AND *D* WHEN APPLIED TO CHAINS *A* AND *B*, RESPECTIVELY.

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Components

#1: Protein/peptide RELAXIN, A-CHAIN


Mass: 2661.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04090
#2: Protein/peptide RELAXIN, B-CHAIN


Mass: 3200.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04090
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNUMBERING OF THE RESIDUES IS BASED ON INSULIN (EG. 1INS OF PROTEIN DATA BANK). WEAK OR NONEXISTENT ...NUMBERING OF THE RESIDUES IS BASED ON INSULIN (EG. 1INS OF PROTEIN DATA BANK). WEAK OR NONEXISTENT ELECTRON DENSITY PREVENTS IDENTIFICATION OF THE FOLLOWING: SOME ATOMS OF PCA A(-3); RESIDUES SER B 25, THR D 23, TRP D 24 AND SER D 25. MULTIPLE ATOMIC POSITIONS ARE INCLUDED FOR SIDE CHAIN ATOMS OF THE FOLLOWING RESIDUES: SER A 15, GLU B 10, TRP B 24, AND ARG C 14.

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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: 39.07 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlrelaxin1drop
2150 mM1reservoirNaCl
310 mMcitrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 13471 / Num. measured all: 50106 / Rmerge(I) obs: 0.063

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.187 / Rfactor obs: 0.187 / Highest resolution: 1.5 Å
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms788 0 0 73 861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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
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
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 8 Å / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d3
X-RAY DIFFRACTIONx_planar_d0.060.061
X-RAY DIFFRACTIONx_plane_restr0.020.014
X-RAY DIFFRACTIONx_chiral_restr0.1250.131
X-RAY DIFFRACTIONx_mcbond_it22.37
X-RAY DIFFRACTIONx_scbond_it33.78
X-RAY DIFFRACTIONx_mcangle_it33.57
X-RAY DIFFRACTIONx_scangle_it4.55.91

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