HEADER IMMUNE SYSTEM 29-APR-21 7EQ3 TITLE APO DIABODY FORM OF CRH2-DIRECTED ANTIBODY 9F8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 9F8 DIABODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS LEPTIN RECEPTOR, ANTAGONIST, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR L.YAN REVDAT 3 09-OCT-24 7EQ3 1 REMARK REVDAT 2 29-NOV-23 7EQ3 1 REMARK REVDAT 1 18-MAY-22 7EQ3 0 JRNL AUTH L.YAN JRNL TITL TALL CYTOKINE RECEPTOR SIGNALING FINE-TUNING THROUGH DIMER JRNL TITL 2 GEOMETRIC RECONSTITUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 7561 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 384 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 3.2900 - 2.8700 0.94 2272 108 0.3191 0.3951 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.99 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 7EQ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1300022005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5406 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7564 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 46.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 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: NULL REMARK 200 STARTING MODEL: 3V6O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.0, 0.2M AMMONIUM REMARK 280 ACETATE AND 16% PEG 10000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 16.67333 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 33.34667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.34667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 16.67333 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: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 ALA A 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 132 CG CD1 CD2 CE1 CE2 CZ 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 SER A 15 -3.99 80.72 REMARK 500 LYS A 64 -64.12 37.00 REMARK 500 HIS A 101 2.54 -158.71 REMARK 500 GLU A 102 -69.87 -102.55 REMARK 500 ILE A 124 114.04 72.92 REMARK 500 ARG A 152 -114.03 55.50 REMARK 500 ALA A 173 -47.04 70.36 REMARK 500 ALA A 206 -168.18 -165.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 ACT A 301 DBREF 7EQ3 A 0 229 PDB 7EQ3 7EQ3 0 229 SEQRES 1 A 230 ALA GLU VAL LYS LEU LEU GLU SER GLY PRO GLY LEU VAL SEQRES 2 A 230 ALA PRO SER GLU SER LEU SER ILE THR CYS THR ILE SER SEQRES 3 A 230 GLY PHE SER LEU THR ASP ASP GLY VAL SER TRP ILE ARG SEQRES 4 A 230 GLN PRO PRO GLY LYS GLY LEU GLU TRP LEU GLY VAL ILE SEQRES 5 A 230 TRP GLY GLY GLY SER THR TYR PHE ASN SER LEU PHE LYS SEQRES 6 A 230 SER ARG LEU SER ILE THR ARG ASP ASN SER LYS SER GLN SEQRES 7 A 230 VAL PHE LEU GLU MET ASP SER LEU GLN THR ASP ASP THR SEQRES 8 A 230 ALA MET TYR TYR CYS ALA LYS HIS ASP GLY HIS GLU THR SEQRES 9 A 230 MET ASP TYR TRP GLY GLN GLY THR SER VAL THR VAL SER SEQRES 10 A 230 SER GLY GLY GLY GLY SER GLU ILE VAL MET THR GLN SER SEQRES 11 A 230 PRO LYS PHE MET SER THR SER ILE GLY ASP ARG VAL ASN SEQRES 12 A 230 ILE THR CYS LYS ALA THR GLN ASN VAL ARG THR ALA VAL SEQRES 13 A 230 THR TRP TYR GLN GLN LYS PRO GLY GLN SER PRO GLN ALA SEQRES 14 A 230 LEU ILE PHE LEU ALA SER ASN ARG HIS THR GLY VAL PRO SEQRES 15 A 230 ALA ARG PHE THR GLY SER GLY SER GLY THR ASP PHE THR SEQRES 16 A 230 LEU THR ILE ASN ASN VAL LYS SER GLU ASP LEU ALA ASP SEQRES 17 A 230 TYR PHE CYS LEU GLN HIS TRP ASN TYR PRO LEU THR PHE SEQRES 18 A 230 GLY SER GLY THR LYS LEU GLU ILE LYS HET ACT A 301 4 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- HELIX 1 AA1 PHE A 63 SER A 65 5 3 HELIX 2 AA2 GLN A 86 THR A 90 5 5 HELIX 3 AA3 LYS A 201 LEU A 205 5 5 SHEET 1 AA1 4 LYS A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N LYS A 3 SHEET 3 AA1 4 GLN A 77 MET A 82 -1 O VAL A 78 N CYS A 22 SHEET 4 AA1 4 LEU A 67 ASP A 72 -1 N THR A 70 O PHE A 79 SHEET 1 AA2 6 LEU A 11 VAL A 12 0 SHEET 2 AA2 6 THR A 111 VAL A 115 1 O THR A 114 N VAL A 12 SHEET 3 AA2 6 ALA A 91 HIS A 98 -1 N TYR A 93 O THR A 111 SHEET 4 AA2 6 VAL A 34 GLN A 39 -1 N ILE A 37 O TYR A 94 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O LEU A 48 N TRP A 36 SHEET 6 AA2 6 THR A 57 PHE A 59 -1 O TYR A 58 N VAL A 50 SHEET 1 AA3 4 LEU A 11 VAL A 12 0 SHEET 2 AA3 4 THR A 111 VAL A 115 1 O THR A 114 N VAL A 12 SHEET 3 AA3 4 ALA A 91 HIS A 98 -1 N TYR A 93 O THR A 111 SHEET 4 AA3 4 MET A 104 TRP A 107 -1 O TYR A 106 N LYS A 97 SHEET 1 AA4 4 MET A 126 SER A 129 0 SHEET 2 AA4 4 VAL A 141 ALA A 147 -1 O LYS A 146 N THR A 127 SHEET 3 AA4 4 ASP A 192 ILE A 197 -1 O LEU A 195 N ILE A 143 SHEET 4 AA4 4 PHE A 184 GLY A 188 -1 N THR A 185 O THR A 196 SHEET 1 AA5 6 PHE A 132 THR A 135 0 SHEET 2 AA5 6 THR A 224 ILE A 228 1 O GLU A 227 N THR A 135 SHEET 3 AA5 6 ASP A 207 GLN A 212 -1 N TYR A 208 O THR A 224 SHEET 4 AA5 6 VAL A 155 GLN A 160 -1 N TYR A 158 O PHE A 209 SHEET 5 AA5 6 GLN A 167 PHE A 171 -1 O LEU A 169 N TRP A 157 SHEET 6 AA5 6 ASN A 175 ARG A 176 -1 O ASN A 175 N PHE A 171 SHEET 1 AA6 4 PHE A 132 THR A 135 0 SHEET 2 AA6 4 THR A 224 ILE A 228 1 O GLU A 227 N THR A 135 SHEET 3 AA6 4 ASP A 207 GLN A 212 -1 N TYR A 208 O THR A 224 SHEET 4 AA6 4 THR A 219 PHE A 220 -1 O THR A 219 N GLN A 212 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.03 SSBOND 2 CYS A 145 CYS A 210 1555 1555 1.91 CISPEP 1 SER A 129 PRO A 130 0 4.00 CISPEP 2 TYR A 216 PRO A 217 0 -3.53 CRYST1 106.806 106.806 50.020 90.00 90.00 120.00 P 31 2 1 6 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 0.009363 0.005406 0.000000 0.00000 SCALE2 0.000000 0.010811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019992 0.00000 CONECT 154 729 CONECT 729 154 CONECT 1087 1588 CONECT 1588 1087 CONECT 1748 1749 1750 1751 CONECT 1749 1748 CONECT 1750 1748 CONECT 1751 1748 MASTER 249 0 1 3 28 0 0 6 1750 1 8 18 END