HEADER HORMONE 25-JUN-19 6PHQ TITLE CRYSTAL STRUCTURE OF GLUCAGON ANALOG FULLY COMPOSED OF D-AMINO ACIDS TITLE 2 WITH 4-BROMO-D-PHENYLALANINE SUBSTITUTIONS AT POSITION 6 AND 22 IN TITLE 3 SPACE GROUP I41 AT 1.1 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-GLUCAGON D-BRPHE 6,22; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS GLUCAGON, GPCR LIGAND, PEPTIDE HORMONE, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR P.A.MROZ,G.GONZALEZ-GUTIERREZ,R.D.DIMARCHI REVDAT 2 15-NOV-23 6PHQ 1 REMARK LINK ATOM REVDAT 1 01-JUL-20 6PHQ 0 JRNL AUTH P.A.MROZ,G.GONZALEZ-GUTIERREZ,R.D.DIMARCHI JRNL TITL HIGH RESOLUTION X-RAY STRUCTURE OF GLUCAGON AND SELECTED JRNL TITL 2 STEREO-INVERSED ANALOGS IN NOVEL CRYSTALLOGRAPHIC PACKING JRNL TITL 3 ARRANGEMENT. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.D.ADAMS,P.V.AFONINE,G.BUNKOCZI,V.B.CHEN,I.W.DAVIS, REMARK 1 AUTH 2 N.ECHOLS,J.J.HEADD,L.W.HUNG,G.J.KAPRAL,R.W.GROSSE-KUNSTLEVE, REMARK 1 AUTH 3 A.J.MCCOY,N.W.MORIARTY,R.OEFFNER,R.J.READ,D.C.RICHARDSON, REMARK 1 AUTH 4 J.S.RICHARDSON,T.C.TERWILLIGER,P.H.ZWART REMARK 1 TITL PHENIX: A COMPREHENSIVE PYTHON-BASED SYSTEM FOR REMARK 1 TITL 2 MACROMOLECULAR STRUCTURE SOLUTION. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 66 213 2010 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 20124702 REMARK 1 DOI 10.1107/S0907444909052925 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15_3459: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 6042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 1.4500 - 1.3200 0.00 0 0 0.0000 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6PHQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000241449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6050 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 20.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 22.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.40700 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 20% PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 20.88500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 20.88500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.21950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 7.60975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.88500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.82925 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.88500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.88500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.21950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 20.88500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 22.82925 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 20.88500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 7.60975 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C DAS A 21 H2 BF7 A 22 1.52 REMARK 500 C DAS A 21 H2 BF7 A 22 1.58 REMARK 500 O HOH A 115 O HOH A 116 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 120 DISTANCE = 6.08 ANGSTROMS DBREF 6PHQ A 4 29 PDB 6PHQ 6PHQ 4 29 SEQRES 1 A 26 GLY DTH BF7 DTH DSN DAS DTY DSN DLY DTY DLE DAS DSN SEQRES 2 A 26 DAR DAR DAL DGN DAS BF7 DVA DGN DTR DLE MED DSG DTH HET DTH A 5 14 HET BF7 A 6 20 HET DTH A 7 14 HET DSN A 8 11 HET DAS A 9 12 HET DTY A 10 21 HET DSN A 11 22 HET DLY A 12 22 HET DTY A 13 21 HET DLE A 14 19 HET DAS A 15 12 HET DSN A 16 22 HET DAR A 17 24 HET DAR A 18 24 HET DAL A 19 10 HET DGN A 20 17 HET DAS A 21 24 HET BF7 A 22 20 HET DVA A 23 16 HET DGN A 24 17 HET DTR A 25 24 HET DLE A 26 19 HET MED A 27 17 HET DSG A 28 14 HET DTH A 29 15 HETNAM DTH D-THREONINE HETNAM BF7 4-BROMO-D-PHENYLALANINE HETNAM DSN D-SERINE HETNAM DAS D-ASPARTIC ACID HETNAM DTY D-TYROSINE HETNAM DLY D-LYSINE HETNAM DLE D-LEUCINE HETNAM DAR D-ARGININE HETNAM DAL D-ALANINE HETNAM DGN D-GLUTAMINE HETNAM DVA D-VALINE HETNAM DTR D-TRYPTOPHAN HETNAM MED D-METHIONINE HETNAM DSG D-ASPARAGINE FORMUL 1 DTH 3(C4 H9 N O3) FORMUL 1 BF7 2(C9 H10 BR N O2) FORMUL 1 DSN 3(C3 H7 N O3) FORMUL 1 DAS 3(C4 H7 N O4) FORMUL 1 DTY 2(C9 H11 N O3) FORMUL 1 DLY C6 H14 N2 O2 FORMUL 1 DLE 2(C6 H13 N O2) FORMUL 1 DAR 2(C6 H15 N4 O2 1+) FORMUL 1 DAL C3 H7 N O2 FORMUL 1 DGN 2(C5 H10 N2 O3) FORMUL 1 DVA C5 H11 N O2 FORMUL 1 DTR C11 H12 N2 O2 FORMUL 1 MED C5 H11 N O2 S FORMUL 1 DSG C4 H8 N2 O3 FORMUL 2 HOH *20(H2 O) HELIX 1 AA1 GLY A 4 DSG A 28 1 25 LINK C GLY A 4 N DTH A 5 1555 1555 1.33 LINK C DTH A 5 N BF7 A 6 1555 1555 1.30 LINK C BF7 A 6 N DTH A 7 1555 1555 1.32 LINK C DTH A 7 N DSN A 8 1555 1555 1.32 LINK C DSN A 8 N DAS A 9 1555 1555 1.33 LINK C DAS A 9 N DTY A 10 1555 1555 1.34 LINK C DTY A 10 N ADSN A 11 1555 1555 1.33 LINK C DTY A 10 N BDSN A 11 1555 1555 1.33 LINK C ADSN A 11 N DLY A 12 1555 1555 1.33 LINK C BDSN A 11 N DLY A 12 1555 1555 1.33 LINK C DLY A 12 N DTY A 13 1555 1555 1.32 LINK C DTY A 13 N DLE A 14 1555 1555 1.31 LINK C DLE A 14 N DAS A 15 1555 1555 1.32 LINK C DAS A 15 N ADSN A 16 1555 1555 1.33 LINK C DAS A 15 N BDSN A 16 1555 1555 1.33 LINK C ADSN A 16 N DAR A 17 1555 1555 1.32 LINK C BDSN A 16 N DAR A 17 1555 1555 1.32 LINK C DAR A 17 N DAR A 18 1555 1555 1.33 LINK C DAR A 18 N DAL A 19 1555 1555 1.32 LINK C DAL A 19 N DGN A 20 1555 1555 1.33 LINK C DGN A 20 N ADAS A 21 1555 1555 1.32 LINK C DGN A 20 N BDAS A 21 1555 1555 1.32 LINK C ADAS A 21 N BF7 A 22 1555 1555 1.32 LINK C BDAS A 21 N BF7 A 22 1555 1555 1.32 LINK C BF7 A 22 N DVA A 23 1555 1555 1.32 LINK C DVA A 23 N DGN A 24 1555 1555 1.32 LINK C DGN A 24 N DTR A 25 1555 1555 1.33 LINK C DTR A 25 N DLE A 26 1555 1555 1.32 LINK C DLE A 26 N MED A 27 1555 1555 1.33 LINK C MED A 27 N DSG A 28 1555 1555 1.33 LINK C DSG A 28 N DTH A 29 1555 1555 1.33 CRYST1 41.770 41.770 30.439 90.00 90.00 90.00 I 41 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.023940 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023940 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032853 0.00000