HEADER PROTEIN BINDING 02-OCT-20 7KBM TITLE REVERSE TRANSCRIPTASE DIABODY WITH R83C MUTATION CRYSTALLIZED IN C2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-CHAIN SCFV; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SCFV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIABODY, IMMUNOGLOBIN, REVERSE TRANSCRIPTASE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.CHESTERMAN,E.ARNOLD REVDAT 3 18-OCT-23 7KBM 1 REMARK REVDAT 2 16-JUN-21 7KBM 1 JRNL REVDAT 1 10-MAR-21 7KBM 0 JRNL AUTH C.CHESTERMAN,E.ARNOLD JRNL TITL CO-CRYSTALLIZATION WITH DIABODIES: A CASE STUDY FOR THE JRNL TITL 2 INTRODUCTION OF SYNTHETIC SYMMETRY. JRNL REF STRUCTURE V. 29 598 2021 JRNL REFN ISSN 0969-2126 JRNL PMID 33636101 JRNL DOI 10.1016/J.STR.2021.02.001 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.14-3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 12421 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 630 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 33.3800 - 3.4100 0.98 2621 141 0.1704 0.2004 REMARK 3 2 3.4100 - 2.7100 0.99 2589 144 0.2062 0.2815 REMARK 3 3 2.7100 - 2.3600 0.97 2547 135 0.2443 0.2848 REMARK 3 4 2.3600 - 2.1500 0.87 2288 120 0.2680 0.3309 REMARK 3 5 2.1500 - 2.0000 0.67 1746 90 0.2849 0.3565 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) : 0.324 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.53 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 1780 REMARK 3 ANGLE : 0.537 2436 REMARK 3 CHIRALITY : 0.042 268 REMARK 3 PLANARITY : 0.003 317 REMARK 3 DIHEDRAL : 2.227 1351 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 7KBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252192. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-18 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13604 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34700 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: PHENIX REMARK 200 STARTING MODEL: 6VRP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE PH REMARK 280 4.5, 30% PEG 300, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.81900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.15100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.81900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.15100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 HOH A 366 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 397 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 442 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 105 REMARK 465 SER A 196 REMARK 465 GLY A 197 REMARK 465 THR A 198 REMARK 465 GLY A 237 REMARK 465 SER A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 HIS A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 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 VAL A 3 CG1 CG2 REMARK 470 SER A 31 OG REMARK 470 LYS A 46 CE NZ REMARK 470 ARG A 61 CG CD NE CZ NH1 NH2 REMARK 470 SER A 77 OG REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 ILE A 103 CG1 CG2 CD1 REMARK 470 THR A 104 OG1 CG2 REMARK 470 VAL A 106 CG1 CG2 REMARK 470 THR A 107 OG1 CG2 REMARK 470 SER A 129 OG REMARK 470 SER A 138 OG REMARK 470 LYS A 168 CG CD CE NZ REMARK 470 LYS A 171 CG CD CE NZ REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 LYS A 232 CD CE NZ REMARK 470 LYS A 236 CG CD CE NZ 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 ASP A 58 -5.78 69.34 REMARK 500 ILE A 103 31.67 -96.19 REMARK 500 SER A 159 -128.83 56.41 REMARK 500 SER A 159 -128.89 56.33 REMARK 500 THR A 180 -47.50 73.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KBM A 1 244 PDB 7KBM 7KBM 1 244 SEQRES 1 A 244 MET GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL SEQRES 2 A 244 GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SEQRES 3 A 244 GLY PHE SER LEU SER THR SER GLY ILE GLY VAL THR TRP SEQRES 4 A 244 VAL ARG GLN ALA PRO GLY LYS GLY LEU GLU TRP LEU ALA SEQRES 5 A 244 THR ILE TRP TRP ASP ASP ASP ASN ARG TYR ALA ASP SER SEQRES 6 A 244 VAL LYS GLY ARG PHE THR ILE SER ALA ASP THR SER LYS SEQRES 7 A 244 ASN THR ALA TYR LEU GLN MET ASN SER LEU CYS ALA GLU SEQRES 8 A 244 ASP THR ALA VAL TYR TYR CYS ALA GLN SER ALA ILE THR SEQRES 9 A 244 SER VAL THR ASP SER ALA MET ASP HIS TRP GLY GLN GLY SEQRES 10 A 244 THR LEU VAL THR VAL SER SER GLY GLY GLY GLY SER ASP SEQRES 11 A 244 ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SER SEQRES 12 A 244 VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER GLN SEQRES 13 A 244 ASP ILE SER SER TYR LEU ASN TRP TYR GLN GLN LYS PRO SEQRES 14 A 244 GLY LYS ALA PRO LYS LEU LEU ILE TYR TYR THR SER SER SEQRES 15 A 244 LEU HIS SER GLY VAL PRO SER ARG PHE SER GLY SER ARG SEQRES 16 A 244 SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU GLN SEQRES 17 A 244 PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN TYR SER SEQRES 18 A 244 LYS PHE PRO TRP THR PHE GLY GLN GLY THR LYS VAL GLU SEQRES 19 A 244 ILE LYS GLY SER HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *143(H2 O) HELIX 1 AA1 ASP A 64 LYS A 67 5 4 HELIX 2 AA2 CYS A 89 THR A 93 5 5 HELIX 3 AA3 GLN A 208 PHE A 212 5 5 SHEET 1 AA1 4 GLN A 4 SER A 8 0 SHEET 2 AA1 4 LEU A 19 SER A 26 -1 O ALA A 24 N VAL A 6 SHEET 3 AA1 4 THR A 80 MET A 85 -1 O ALA A 81 N CYS A 23 SHEET 4 AA1 4 PHE A 70 ASP A 75 -1 N SER A 73 O TYR A 82 SHEET 1 AA2 6 GLY A 11 VAL A 13 0 SHEET 2 AA2 6 THR A 118 VAL A 122 1 O LEU A 119 N GLY A 11 SHEET 3 AA2 6 ALA A 94 ALA A 102 -1 N ALA A 94 O VAL A 120 SHEET 4 AA2 6 ILE A 35 GLN A 42 -1 N VAL A 40 O TYR A 97 SHEET 5 AA2 6 LEU A 48 TRP A 55 -1 O ILE A 54 N VAL A 37 SHEET 6 AA2 6 ASN A 60 TYR A 62 -1 O ARG A 61 N THR A 53 SHEET 1 AA3 4 GLY A 11 VAL A 13 0 SHEET 2 AA3 4 THR A 118 VAL A 122 1 O LEU A 119 N GLY A 11 SHEET 3 AA3 4 ALA A 94 ALA A 102 -1 N ALA A 94 O VAL A 120 SHEET 4 AA3 4 MET A 111 ASP A 112 -1 O ASP A 112 N GLN A 100 SHEET 1 AA4 4 MET A 133 SER A 136 0 SHEET 2 AA4 4 VAL A 148 ALA A 154 -1 O THR A 151 N SER A 136 SHEET 3 AA4 4 PHE A 200 ILE A 204 -1 O LEU A 202 N ILE A 150 SHEET 4 AA4 4 PHE A 191 SER A 194 -1 N SER A 192 O THR A 203 SHEET 1 AA5 6 SER A 139 ALA A 142 0 SHEET 2 AA5 6 THR A 231 ILE A 235 1 O GLU A 234 N LEU A 140 SHEET 3 AA5 6 THR A 214 GLN A 219 -1 N TYR A 215 O THR A 231 SHEET 4 AA5 6 LEU A 162 GLN A 167 -1 N TYR A 165 O TYR A 216 SHEET 5 AA5 6 LYS A 174 TYR A 178 -1 O LEU A 176 N TRP A 164 SHEET 6 AA5 6 SER A 182 LEU A 183 -1 O SER A 182 N TYR A 178 SHEET 1 AA6 4 SER A 139 ALA A 142 0 SHEET 2 AA6 4 THR A 231 ILE A 235 1 O GLU A 234 N LEU A 140 SHEET 3 AA6 4 THR A 214 GLN A 219 -1 N TYR A 215 O THR A 231 SHEET 4 AA6 4 THR A 226 PHE A 227 -1 O THR A 226 N GLN A 219 SSBOND 1 CYS A 23 CYS A 98 1555 1555 2.02 SSBOND 2 CYS A 89 CYS A 89 1555 2555 2.01 SSBOND 3 CYS A 152 CYS A 217 1555 1555 2.04 CISPEP 1 SER A 136 PRO A 137 0 -4.28 CISPEP 2 PHE A 223 PRO A 224 0 1.17 CRYST1 73.638 86.302 36.249 90.00 116.50 90.00 C 1 2 1 4 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 0.013580 0.000000 0.006771 0.00000 SCALE2 0.000000 0.011587 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030826 0.00000