HEADER DE NOVO PROTEIN 04-DEC-19 6V67 TITLE APO STRUCTURE OF THE DE NOVO PD-1 BINDING MINIPROTEIN GR918.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PD-1 BINDING MINIPROTEIN GR918.2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: EXPI293F KEYWDS PD-1, DISULFIDE MINIPROTEIN, COMPUTATIONAL DESIGN, BINDER, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BICK,C.M.BRYAN,D.BAKER,F.DIMAIO,A.KANG REVDAT 3 03-APR-24 6V67 1 REMARK REVDAT 2 29-DEC-21 6V67 1 JRNL REVDAT 1 09-DEC-20 6V67 0 JRNL AUTH C.M.BRYAN,G.J.ROCKLIN,M.J.BICK,A.FORD,S.MAJRI-MORRISON, JRNL AUTH 2 A.V.KROLL,C.J.MILLER,L.CARTER,I.GORESHNIK,A.KANG,F.DIMAIO, JRNL AUTH 3 K.V.TARBELL,D.BAKER JRNL TITL COMPUTATIONAL DESIGN OF A SYNTHETIC PD-1 AGONIST. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 34272285 JRNL DOI 10.1073/PNAS.2102164118 REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2849 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) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 29628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1465 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 50.8050 - 2.3052 0.98 2930 155 0.1611 0.1481 REMARK 3 2 2.3052 - 1.8297 0.98 2842 156 0.1444 0.1491 REMARK 3 3 1.8297 - 1.5984 0.99 2841 166 0.1342 0.1377 REMARK 3 4 1.5984 - 1.4522 0.98 2818 151 0.1204 0.1396 REMARK 3 5 1.4522 - 1.3481 0.98 2829 143 0.1190 0.1418 REMARK 3 6 1.3481 - 1.2686 0.99 2863 154 0.1207 0.1486 REMARK 3 7 1.2686 - 1.2051 0.98 2794 130 0.1285 0.1574 REMARK 3 8 1.2051 - 1.1526 0.97 2760 148 0.1368 0.1687 REMARK 3 9 1.1526 - 1.1082 0.96 2757 136 0.1495 0.1707 REMARK 3 10 1.1082 - 1.0700 0.95 2729 126 0.1981 0.2551 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.00 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 : 0.009 769 REMARK 3 ANGLE : 1.084 1058 REMARK 3 CHIRALITY : 0.099 105 REMARK 3 PLANARITY : 0.006 142 REMARK 3 DIHEDRAL : 15.344 298 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 6V67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MAY 1, 2016 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.23 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33643 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 50.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.59300 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 2.7.18 REMARK 200 STARTING MODEL: SINGLE HELIX, RESIDUES 18-31, OF THE COMPUTATIONAL REMARK 200 MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES/IMIDAZOLE PH 6.5, 0.03 M REMARK 280 DIETHYLENE GLYCOL, 0.03 M TRIETHYLENE GLYCOL, 0.03 M REMARK 280 TETRAETHYLENE GLYCOL, 0.03 M PENTAETHYLENE GLYCOL, 10% PEG 20, REMARK 280 000, 20% PEG MME 550, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K 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 25.42450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.37200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.42450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.37200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 HOH A 108 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 118 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 109 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 GLY A 1 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 SER A 2 OG REMARK 470 LYS A 25 CD CE NZ REMARK 470 GLU A 29 CD OE1 OE2 REMARK 470 LYS A 33 CE NZ REMARK 470 GLN A 42 CD OE1 NE2 REMARK 470 SER B 2 OG REMARK 470 LYS B 25 CD CE NZ REMARK 470 LYS B 33 CD CE NZ REMARK 470 GLN B 42 CD OE1 NE2 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 HH TYR A 17 OH TYR B 15 1.31 REMARK 500 O HOH A 109 O HOH A 141 2.10 REMARK 500 OH TYR A 17 OH TYR B 15 2.11 REMARK 500 O HOH A 111 O HOH B 114 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 140 O HOH A 140 2656 1.80 REMARK 500 REMARK 500 REMARK: NULL DBREF 6V67 A 1 43 PDB 6V67 6V67 1 43 DBREF 6V67 B 1 43 PDB 6V67 6V67 1 43 SEQRES 1 A 43 GLY SER CYS PHE CYS VAL CYS ILE THR GLY PRO GLN TRP SEQRES 2 A 43 ASP TYR ARG TYR GLY ASN LYS GLU GLN CYS LYS LYS PHE SEQRES 3 A 43 LEU THR GLU CYS GLU GLN LYS ASN PRO GLY ALA GLU VAL SEQRES 4 A 43 GLU ILE GLN CYS SEQRES 1 B 43 GLY SER CYS PHE CYS VAL CYS ILE THR GLY PRO GLN TRP SEQRES 2 B 43 ASP TYR ARG TYR GLY ASN LYS GLU GLN CYS LYS LYS PHE SEQRES 3 B 43 LEU THR GLU CYS GLU GLN LYS ASN PRO GLY ALA GLU VAL SEQRES 4 B 43 GLU ILE GLN CYS FORMUL 3 HOH *88(H2 O) HELIX 1 AA1 ASN A 19 ASN A 34 1 16 HELIX 2 AA2 ASN B 19 ASN B 34 1 16 SHEET 1 AA1 6 GLU A 38 GLN A 42 0 SHEET 2 AA1 6 CYS A 3 THR A 9 -1 N ILE A 8 O GLU A 38 SHEET 3 AA1 6 GLN A 12 GLY A 18 -1 O GLY A 18 N CYS A 3 SHEET 4 AA1 6 GLN B 12 GLY B 18 -1 O TRP B 13 N TYR A 17 SHEET 5 AA1 6 CYS B 3 THR B 9 -1 N CYS B 3 O GLY B 18 SHEET 6 AA1 6 GLU B 38 GLN B 42 -1 O GLU B 38 N ILE B 8 SSBOND 1 CYS A 3 CYS A 43 1555 1555 2.03 SSBOND 2 CYS A 5 CYS A 23 1555 1555 2.05 SSBOND 3 CYS A 7 CYS A 30 1555 1555 2.04 SSBOND 4 CYS B 3 CYS B 43 1555 1555 2.05 SSBOND 5 CYS B 5 CYS B 23 1555 1555 2.05 SSBOND 6 CYS B 7 CYS B 30 1555 1555 2.02 CRYST1 50.849 26.744 51.537 90.00 99.67 90.00 C 1 2 1 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 0.019666 0.000000 0.003350 0.00000 SCALE2 0.000000 0.037392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019683 0.00000