HEADER DE NOVO PROTEIN 19-AUG-20 7A48 TITLE CRYSTAL STRUCTURE OF THE APH COILED-COIL IN COMPLEX WITH NB49 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY 49; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: APH COLIED-COIL; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS COILED-COIL, NANOBODY, ANTIBODY, PROTEIN DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.HADZI REVDAT 3 01-MAY-24 7A48 1 REMARK REVDAT 2 11-AUG-21 7A48 1 REMARK REVDAT 1 05-MAY-21 7A48 0 JRNL AUTH A.MAJERLE,S.HADZI,J.AUPIC,T.SATLER,F.LAPENTA,Z.STRMSEK, JRNL AUTH 2 J.LAH,R.LORIS,R.JERALA JRNL TITL A NANOBODY TOOLBOX TARGETING DIMERIC COILED-COIL MODULES FOR JRNL TITL 2 FUNCTIONALIZATION OF DESIGNED PROTEIN ORIGAMI STRUCTURES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33893235 JRNL DOI 10.1073/PNAS.2021899118 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 18080 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 905 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 2.8103 - 2.2307 0.98 2887 152 0.2002 0.2290 REMARK 3 2 2.2307 - 1.9487 0.98 2903 153 0.1807 0.2090 REMARK 3 3 1.9487 - 1.7705 0.98 2882 152 0.2055 0.2737 REMARK 3 4 1.7705 - 1.6436 0.98 2836 149 0.2378 0.2834 REMARK 3 5 1.6436 - 1.5470 0.91 2666 141 0.2459 0.2976 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.93 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 1325 REMARK 3 ANGLE : 0.855 1800 REMARK 3 CHIRALITY : 0.048 192 REMARK 3 PLANARITY : 0.005 238 REMARK 3 DIHEDRAL : 2.569 974 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 2 THROUGH 121) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4942 -29.1832 13.9456 REMARK 3 T TENSOR REMARK 3 T11: 0.1385 T22: 0.1518 REMARK 3 T33: 0.0936 T12: 0.0204 REMARK 3 T13: -0.0421 T23: -0.0145 REMARK 3 L TENSOR REMARK 3 L11: 3.6667 L22: 2.5437 REMARK 3 L33: 2.6289 L12: 0.9281 REMARK 3 L13: -0.3752 L23: 0.2216 REMARK 3 S TENSOR REMARK 3 S11: -0.0738 S12: -0.3441 S13: 0.1228 REMARK 3 S21: 0.0101 S22: 0.0213 S23: 0.0090 REMARK 3 S31: -0.0955 S32: 0.0671 S33: 0.0219 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 42) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0557 -33.6828 2.5936 REMARK 3 T TENSOR REMARK 3 T11: 0.1914 T22: 0.2359 REMARK 3 T33: 0.1740 T12: 0.0007 REMARK 3 T13: -0.0347 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 3.6744 L22: 1.2282 REMARK 3 L33: 6.4543 L12: 0.9504 REMARK 3 L13: -3.3897 L23: -0.9585 REMARK 3 S TENSOR REMARK 3 S11: -0.2674 S12: 0.0807 S13: -0.2340 REMARK 3 S21: -0.1283 S22: -0.0834 S23: -0.1698 REMARK 3 S31: 0.2417 S32: 0.2662 S33: 0.1307 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 7A48 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1292110827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978570 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18085 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.547 REMARK 200 RESOLUTION RANGE LOW (A) : 44.735 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.110 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 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: MODELLER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULPHATE, 0.1 M SODIUM REMARK 280 ACETATE PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 47.29000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.03500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.29000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.03500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 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 TYR A 121 REMARK 465 PRO A 122 REMARK 465 TYR A 123 REMARK 465 ASP A 124 REMARK 465 VAL A 125 REMARK 465 PRO A 126 REMARK 465 ASP A 127 REMARK 465 TYR A 128 REMARK 465 GLY A 129 REMARK 465 SER A 130 REMARK 465 GLY A 131 REMARK 465 ARG A 132 REMARK 465 ALA A 133 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 GLN A 1 CG CD OE1 NE2 REMARK 470 ARG A 27 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 107 CG CD1 CD2 CE1 CE2 CZ OH 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 VAL A 48 -51.04 -121.05 REMARK 500 ASP A 101 -159.73 -157.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 7A48 A 1 133 PDB 7A48 7A48 1 133 DBREF 7A48 B 0 41 PDB 7A48 7A48 0 41 SEQRES 1 A 133 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 133 PRO GLY GLY SER LEU ARG LEU SER CYS ILE ALA SER GLY SEQRES 3 A 133 ARG THR PHE ASN PRO TYR GLY MET GLY TRP PHE ARG GLN SEQRES 4 A 133 VAL PRO GLY LYS GLU ARG THR PHE VAL SER GLY ILE THR SEQRES 5 A 133 TRP ILE GLY GLY THR THR TYR TYR VAL ASN SER VAL LYS SEQRES 6 A 133 GLY ARG PHE THR ILE SER ARG ASP ARG ALA LYS ASN THR SEQRES 7 A 133 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 133 ALA VAL TYR TYR CYS ALA ALA ASP LYS ASP ASN THR GLY SEQRES 9 A 133 TYR ASN TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 10 A 133 SER PHE GLY TYR PRO TYR ASP VAL PRO ASP TYR GLY SER SEQRES 11 A 133 GLY ARG ALA SEQRES 1 B 42 ACE LEU GLU GLU GLU LEU LYS GLN LEU GLU GLU GLU LEU SEQRES 2 B 42 GLN ALA ILE GLU GLU GLN LEU ALA GLN LEU GLN TRP LYS SEQRES 3 B 42 ALA GLN ALA ARG LYS GLU LYS LEU ALA GLN LEU LYS GLU SEQRES 4 B 42 LYS LEU NH2 HET ACE B 0 3 HET NH2 B 41 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 2 ACE C2 H4 O FORMUL 2 NH2 H2 N FORMUL 3 HOH *96(H2 O) HELIX 1 AA1 ASN A 62 LYS A 65 5 4 HELIX 2 AA2 LYS A 87 THR A 91 5 5 HELIX 3 AA3 LEU B 1 LEU B 40 1 40 SHEET 1 AA1 4 VAL A 2 SER A 7 0 SHEET 2 AA1 4 LEU A 18 GLY A 26 -1 O SER A 21 N SER A 7 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N THR A 69 O GLN A 82 SHEET 1 AA2 6 GLY A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 112 VAL A 116 1 O THR A 115 N GLY A 10 SHEET 3 AA2 6 ALA A 92 ASP A 99 -1 N TYR A 94 O THR A 112 SHEET 4 AA2 6 GLY A 33 GLN A 39 -1 N PHE A 37 O TYR A 95 SHEET 5 AA2 6 THR A 46 THR A 52 -1 O SER A 49 N TRP A 36 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O TYR A 59 N GLY A 50 SHEET 1 AA3 4 GLY A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 112 VAL A 116 1 O THR A 115 N GLY A 10 SHEET 3 AA3 4 ALA A 92 ASP A 99 -1 N TYR A 94 O THR A 112 SHEET 4 AA3 4 TYR A 107 TRP A 108 -1 O TYR A 107 N ALA A 98 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.16 LINK C ACE B 0 N LEU B 1 1555 1555 1.33 LINK C LEU B 40 N NH2 B 41 1555 1555 1.33 CRYST1 94.580 26.070 54.250 90.00 108.92 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 0.010573 0.000000 0.003624 0.00000 SCALE2 0.000000 0.038358 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019486 0.00000