HEADER HORMONE 06-SEP-22 8GSG TITLE T3R3 FORM OF HUMAN INSULIN WITH SINGLE ZN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN A CHAIN; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: SMALL CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: INSULIN B CHAIN; COMPND 8 CHAIN: B, D; COMPND 9 SYNONYM: LARGE CHAIN; COMPND 10 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; 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; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR Z.L.ZHU REVDAT 2 29-NOV-23 8GSG 1 REMARK REVDAT 1 15-MAR-23 8GSG 0 JRNL AUTH Z.L.ZHU JRNL TITL T3R3 INSULIN WITH SINGLE ZN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 5396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 245 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 17.5300 - 2.5800 1.00 2585 127 0.1668 0.1831 REMARK 3 2 2.5800 - 2.0500 0.99 2566 118 0.1843 0.2615 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) : 0.183 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.086 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.44 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 : 0.004 854 REMARK 3 ANGLE : 0.690 1155 REMARK 3 CHIRALITY : 0.038 125 REMARK 3 PLANARITY : 0.003 148 REMARK 3 DIHEDRAL : 15.429 291 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 8GSG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300032020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4-7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5407 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 17.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.04358 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.16950 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: 1TRZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH7.5,10% (V/V) PEG 6000, REMARK 280 5% (V/V) MPD, VAPOR DIFFUSION, SITTING DROP, 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 40.00900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.09921 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.07633 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 40.00900 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 23.09921 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 12.07633 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 40.00900 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 23.09921 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 12.07633 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.19841 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 24.15267 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 46.19841 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 24.15267 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 46.19841 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 24.15267 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -416.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 ZN ZN D 101 LIES ON A SPECIAL POSITION. REMARK 375 CL CL D 102 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 217 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 218 LIES ON A SPECIAL POSITION. 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 65.71 -108.77 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 B 218 DISTANCE = 5.95 ANGSTROMS 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 NA C 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 30 OG1 REMARK 620 2 GLU C 17 OE1 24.1 REMARK 620 3 GLU C 17 OE2 25.2 2.0 REMARK 620 N 1 2 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 8GSG A 1 21 UNP P01308 INS_HUMAN 90 110 DBREF 8GSG B 1 30 UNP P01308 INS_HUMAN 25 54 DBREF 8GSG C 1 21 UNP P01308 INS_HUMAN 90 110 DBREF 8GSG D 1 30 UNP P01308 INS_HUMAN 25 54 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 ASN SEQRES 1 B 30 PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU SEQRES 2 B 30 ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR SEQRES 3 B 30 THR PRO LYS THR 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 ASN SEQRES 1 D 30 PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU SEQRES 2 D 30 ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR SEQRES 3 D 30 THR PRO LYS THR HET CRS B 101 16 HET CRS C 101 8 HET NA C 102 1 HET ZN D 101 1 HET CL D 102 1 HETNAM CRS M-CRESOL HETNAM NA SODIUM ION HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 5 CRS 2(C7 H8 O) FORMUL 7 NA NA 1+ FORMUL 8 ZN ZN 2+ FORMUL 9 CL CL 1- FORMUL 10 HOH *69(H2 O) HELIX 1 AA1 GLY A 1 CYS A 7 1 7 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 GLY B 8 GLY B 20 1 13 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 TYR D 26 N PHE B 24 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 OG1 THR B 30 NA NA C 102 1555 6445 2.33 LINK OE1 GLU C 17 NA NA C 102 1555 1555 2.28 LINK OE2 GLU C 17 NA NA C 102 1555 1555 2.47 LINK NE2 HIS D 10 ZN ZN D 101 1555 1555 2.31 LINK NE2 HIS D 10 ZN ZN D 101 1555 2555 2.16 CRYST1 80.018 80.018 36.229 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 0.012497 0.007215 0.000000 0.00000 SCALE2 0.000000 0.014431 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027602 0.00000