HEADER HORMONE 19-OCT-23 8WU0 TITLE CRYSTAL STRUCTURE OF LISARGINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: INSULIN; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: INS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: INS; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS INSULIN ANALOGUE, LONG ACTING, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR P.WANG,Z.ZHU REVDAT 1 23-OCT-24 8WU0 0 JRNL AUTH P.WANG,Z.ZHU JRNL TITL CRYSTAL STRUCTURE OF LISARGINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.ZHU,P.WANG REMARK 1 TITL MACROMOLECULAR STRUCTURE DETERMINATION USING X-RAYS, REMARK 1 TITL 2 NEUTRONS AND ELECTRONS: RECENT DEVELOPMENTS IN PHENIX REMARK 1 REF ACTA CRYSTALLOGR., SECT. D: V. 75 861 2019 REMARK 1 REF 2 BIOL. CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 35.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 6844 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 343 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 39.5000 - 2.4600 0.95 3278 157 0.1992 0.2105 REMARK 3 2 2.4600 - 1.9500 0.94 3223 186 0.3242 0.3617 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 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) : 46.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.40 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 : 0.002 816 REMARK 3 ANGLE : 0.399 1102 REMARK 3 CHIRALITY : 0.033 122 REMARK 3 PLANARITY : 0.002 140 REMARK 3 DIHEDRAL : 12.579 282 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 8WU0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300042005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3-7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97774 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6844 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 39.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 38.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (V/V) 2-PROPANOL, 0.2 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, 0.1 M HEPES SODIUM PH 7.5, REMARK 280 EVAPORATION, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.49550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.80274 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.47700 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 39.49550 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 22.80274 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.47700 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 39.49550 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 22.80274 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.47700 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.60548 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 26.95400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 45.60548 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.95400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 45.60548 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 26.95400 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL B 102 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN D 101 LIES ON A SPECIAL POSITION. REMARK 375 CL CL D 102 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 209 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 206 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 207 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS B 31 REMARK 465 ARG B 32 REMARK 465 LYS D 31 REMARK 465 ARG D 32 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 OE1 GLN A 5 OH TYR A 19 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS D 29 59.27 -90.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 10 NE2 REMARK 620 2 HIS B 10 NE2 0.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 10 NE2 REMARK 620 2 HIS D 10 NE2 0.0 REMARK 620 N 1 DBREF 8WU0 A 1 20 UNP P01308 INS_HUMAN 90 109 DBREF 8WU0 B 1 32 UNP P01308 INS_HUMAN 25 56 DBREF 8WU0 C 1 20 UNP P01308 INS_HUMAN 90 109 DBREF 8WU0 D 1 32 UNP P01308 INS_HUMAN 25 56 SEQADV 8WU0 GLY A 21 UNP P01308 EXPRESSION TAG SEQADV 8WU0 LYS B 31 UNP P01308 ARG 55 CONFLICT SEQADV 8WU0 GLY C 21 UNP P01308 EXPRESSION TAG SEQADV 8WU0 LYS D 31 UNP P01308 ARG 55 CONFLICT SEQRES 1 A 21 GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU SEQRES 2 A 21 TYR GLN LEU GLU ASN TYR CYS GLY SEQRES 1 B 32 PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU SEQRES 2 B 32 ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR SEQRES 3 B 32 THR PRO LYS THR LYS ARG SEQRES 1 C 21 GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU SEQRES 2 C 21 TYR GLN LEU GLU ASN TYR CYS GLY SEQRES 1 D 32 PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU SEQRES 2 D 32 ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR SEQRES 3 D 32 THR PRO LYS THR LYS ARG HET ZN B 101 1 HET CL B 102 1 HET ZN D 101 1 HET CL D 102 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 5 ZN 2(ZN 2+) FORMUL 6 CL 2(CL 1-) FORMUL 9 HOH *27(H2 O) HELIX 1 AA1 GLY A 1 THR A 8 1 8 HELIX 2 AA2 SER A 12 GLU A 17 1 6 HELIX 3 AA3 ASN A 18 CYS A 20 5 3 HELIX 4 AA4 VAL B 2 GLY B 20 1 19 HELIX 5 AA5 GLU B 21 GLY B 23 5 3 HELIX 6 AA6 ILE C 2 CYS C 7 1 6 HELIX 7 AA7 SER C 12 GLU C 17 1 6 HELIX 8 AA8 ASN C 18 CYS C 20 5 3 HELIX 9 AA9 VAL D 2 GLY D 20 1 19 HELIX 10 AB1 GLU D 21 GLY D 23 5 3 SHEET 1 AA1 2 PHE B 24 TYR B 26 0 SHEET 2 AA1 2 PHE D 24 TYR D 26 -1 O PHE D 24 N TYR B 26 SSBOND 1 CYS A 6 CYS A 11 1555 1555 2.03 SSBOND 2 CYS A 7 CYS B 7 1555 1555 2.03 SSBOND 3 CYS A 20 CYS B 19 1555 1555 2.03 SSBOND 4 CYS C 6 CYS C 11 1555 1555 2.03 SSBOND 5 CYS C 7 CYS D 7 1555 1555 2.03 SSBOND 6 CYS C 20 CYS D 19 1555 1555 2.03 LINK NE2 HIS B 10 ZN ZN B 101 1555 1555 2.30 LINK NE2 HIS B 10 ZN ZN B 101 1555 3555 2.07 LINK NE2 HIS D 10 ZN ZN D 101 1555 1555 2.30 LINK NE2 HIS D 10 ZN ZN D 101 1555 2555 2.13 CRYST1 78.991 78.991 40.431 90.00 90.00 120.00 H 3 18 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 0.012660 0.007309 0.000000 0.00000 SCALE2 0.000000 0.014618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024733 0.00000 CONECT 43 76 CONECT 49 219 CONECT 76 43 CONECT 154 309 CONECT 219 49 CONECT 239 805 CONECT 309 154 CONECT 445 478 CONECT 451 621 CONECT 478 445 CONECT 556 711 CONECT 621 451 CONECT 641 807 CONECT 711 556 CONECT 805 239 CONECT 807 641 MASTER 289 0 4 10 2 0 0 6 831 4 16 10 END