HEADER SIGNALING PROTEIN 24-SEP-15 5DXW TITLE CRYSTAL STRUCTURE OF MOUSE PD-L1 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PD-L1 NANOBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELIDAE; SOURCE 3 ORGANISM_TAXID: 9835; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IG FOLD, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,D.SAMANTA,S.C.ALMO,H.PLOEGH,J.INGRAM,M.DOUGAN REVDAT 5 23-OCT-24 5DXW 1 REMARK REVDAT 4 27-SEP-23 5DXW 1 REMARK REVDAT 3 30-JAN-19 5DXW 1 SOURCE KEYWDS REMARK REVDAT 2 02-MAR-16 5DXW 1 AUTHOR REVDAT 1 07-OCT-15 5DXW 0 JRNL AUTH A.A.FEDOROV,E.V.FEDOROV,D.SAMANTA,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF MOUSE PD-L1 NANOBODY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 30989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.080 REMARK 3 FREE R VALUE TEST SET COUNT : 689 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 18.2328 - 2.9933 0.99 3322 130 0.1385 0.1323 REMARK 3 2 2.9933 - 2.3776 1.00 3353 123 0.1607 0.2043 REMARK 3 3 2.3776 - 2.0775 1.00 3335 125 0.1529 0.2186 REMARK 3 4 2.0775 - 1.8878 1.00 3334 154 0.1572 0.1767 REMARK 3 5 1.8878 - 1.7526 1.00 3309 134 0.1732 0.2278 REMARK 3 6 1.7526 - 1.6493 1.00 3307 144 0.1968 0.2261 REMARK 3 7 1.6493 - 1.5668 1.00 3319 160 0.2138 0.2483 REMARK 3 8 1.5668 - 1.4986 1.00 3327 142 0.2660 0.3034 REMARK 3 9 1.4986 - 1.4410 0.95 3118 153 0.3126 0.3192 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 940 REMARK 3 ANGLE : 1.067 1277 REMARK 3 CHIRALITY : 0.076 137 REMARK 3 PLANARITY : 0.005 166 REMARK 3 DIHEDRAL : 12.018 342 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 73.9732 1.2282 31.1489 REMARK 3 T TENSOR REMARK 3 T11: 0.0223 T22: 0.0513 REMARK 3 T33: 0.0535 T12: 0.0042 REMARK 3 T13: -0.0050 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 1.3893 L22: 1.2578 REMARK 3 L33: 2.1791 L12: 0.0252 REMARK 3 L13: -0.4295 L23: -0.2341 REMARK 3 S TENSOR REMARK 3 S11: 0.0285 S12: 0.0035 S13: 0.0316 REMARK 3 S21: -0.0046 S22: 0.0207 S23: -0.0376 REMARK 3 S31: -0.0428 S32: -0.0399 S33: -0.0384 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 5DXW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30989 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.441 REMARK 200 RESOLUTION RANGE LOW (A) : 18.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: 1OL0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, AMMONIUM SULFATE, HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 42.59550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.83950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.59550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 14.83950 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, 3 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 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 TOTAL BURIED SURFACE AREA: 330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 170.38200 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 S SO4 A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 350 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 378 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 ALA A 2 REMARK 465 GLY A 117 REMARK 465 GLY A 118 REMARK 465 LEU A 119 REMARK 465 PRO A 120 REMARK 465 GLU A 121 REMARK 465 THR A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 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 ALA A 94 168.69 179.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 DBREF 5DXW A 1 130 PDB 5DXW 5DXW 1 130 SEQRES 1 A 130 MET ALA GLN VAL GLN LEU VAL GLU THR GLY GLY GLY LEU SEQRES 2 A 130 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS THR ALA SEQRES 3 A 130 SER GLY PHE THR PHE SER MET HIS ALA MET THR TRP TYR SEQRES 4 A 130 ARG GLN ALA PRO GLY LYS GLN ARG GLU LEU VAL ALA VAL SEQRES 5 A 130 ILE THR SER HIS GLY ASP ARG ALA ASN TYR THR ASP SER SEQRES 6 A 130 VAL ARG GLY ARG PHE THR ILE SER ARG ASP ASN THR LYS SEQRES 7 A 130 ASN MET VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU SEQRES 8 A 130 ASP THR ALA VAL TYR TYR CYS ASN VAL PRO ARG TYR ASP SEQRES 9 A 130 SER TRP GLY GLN GLY THR GLN VAL THR VAL SER SER GLY SEQRES 10 A 130 GLY LEU PRO GLU THR GLY GLY HIS HIS HIS HIS HIS HIS HET SO4 A 201 5 HET SO4 A 202 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *91(H2 O) HELIX 1 AA1 THR A 30 HIS A 34 5 5 HELIX 2 AA2 ASP A 64 ARG A 67 5 4 HELIX 3 AA3 LYS A 89 THR A 93 5 5 SHEET 1 AA1 4 GLN A 5 THR A 9 0 SHEET 2 AA1 4 LEU A 20 SER A 27 -1 O SER A 27 N GLN A 5 SHEET 3 AA1 4 MET A 80 MET A 85 -1 O MET A 85 N LEU A 20 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 12 VAL A 14 0 SHEET 2 AA2 6 THR A 110 VAL A 114 1 O THR A 113 N GLY A 12 SHEET 3 AA2 6 ALA A 94 VAL A 100 -1 N TYR A 96 O THR A 110 SHEET 4 AA2 6 MET A 36 GLN A 41 -1 N TYR A 39 O TYR A 97 SHEET 5 AA2 6 GLU A 48 ILE A 53 -1 O GLU A 48 N ARG A 40 SHEET 6 AA2 6 ALA A 60 TYR A 62 -1 O ASN A 61 N VAL A 52 SHEET 1 AA3 4 GLY A 12 VAL A 14 0 SHEET 2 AA3 4 THR A 110 VAL A 114 1 O THR A 113 N GLY A 12 SHEET 3 AA3 4 ALA A 94 VAL A 100 -1 N TYR A 96 O THR A 110 SHEET 4 AA3 4 SER A 105 TRP A 106 -1 O SER A 105 N VAL A 100 SSBOND 1 CYS A 24 CYS A 98 1555 1555 2.04 SITE 1 AC1 3 HIS A 34 ALA A 35 ARG A 102 SITE 1 AC2 6 PHE A 29 THR A 30 HIS A 34 LYS A 45 SITE 2 AC2 6 ARG A 102 TYR A 103 CRYST1 85.191 29.679 35.268 90.00 90.00 90.00 P 21 21 2 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 0.011738 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028354 0.00000