HEADER PEPTIDE BINDING PROTEIN 21-MAR-16 5IVO TITLE BC2 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: BC2-NANOBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_COMMON: ALPACA; SOURCE 4 ORGANISM_TAXID: 30538; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOBODY, TAG, CAPTURE, AFFINITY, CATENIN, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.B.BRAUN,T.STEHLE REVDAT 3 10-JAN-24 5IVO 1 REMARK REVDAT 2 28-SEP-16 5IVO 1 REVDAT 1 06-APR-16 5IVO 0 JRNL AUTH M.B.BRAUN,B.TRAENKLE,P.A.KOCH,F.EMELE,F.WEISS,O.POETZ, JRNL AUTH 2 T.STEHLE,U.ROTHBAUER JRNL TITL PEPTIDES IN HEADLOCK - A NOVEL HIGH-AFFINITY AND VERSATILE JRNL TITL 2 PEPTIDE-BINDING NANOBODY FOR PROTEOMICS AND MICROSCOPY. JRNL REF SCI REP V. 6 19211 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 26791954 JRNL DOI 10.1038/SREP19211 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9930 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1192 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 38.9089 - 3.7435 1.00 1055 144 0.1774 0.2095 REMARK 3 2 3.7435 - 2.9716 1.00 984 135 0.1669 0.2089 REMARK 3 3 2.9716 - 2.5961 1.00 974 132 0.1874 0.2079 REMARK 3 4 2.5961 - 2.3588 1.00 973 133 0.2015 0.2378 REMARK 3 5 2.3588 - 2.1897 1.00 962 131 0.1725 0.2203 REMARK 3 6 2.1897 - 2.0606 1.00 949 130 0.1798 0.2088 REMARK 3 7 2.0606 - 1.9574 1.00 954 130 0.1988 0.2477 REMARK 3 8 1.9574 - 1.8722 1.00 947 129 0.2378 0.2589 REMARK 3 9 1.8722 - 1.8001 0.99 940 128 0.2921 0.3159 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.580 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 : 0.014 935 REMARK 3 ANGLE : 1.414 1280 REMARK 3 CHIRALITY : 0.084 138 REMARK 3 PLANARITY : 0.006 167 REMARK 3 DIHEDRAL : 16.732 327 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.6362 1.6038 -3.8407 REMARK 3 T TENSOR REMARK 3 T11: 0.1140 T22: 0.1161 REMARK 3 T33: 0.1262 T12: 0.0150 REMARK 3 T13: -0.0137 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.6510 L22: 2.6522 REMARK 3 L33: 1.4611 L12: 0.1477 REMARK 3 L13: -0.8303 L23: 0.9570 REMARK 3 S TENSOR REMARK 3 S11: 0.0355 S12: -0.0695 S13: -0.2097 REMARK 3 S21: -0.1143 S22: 0.0458 S23: -0.0748 REMARK 3 S31: 0.1041 S32: 0.0457 S33: 0.0369 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 5IVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219461. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918409 REMARK 200 MONOCHROMATOR : KMC-1 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9931 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 38.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 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: 2X1O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES/IMIDAZOLE, 2-METHYL-2,4 REMARK 280 -PENTANEDIOL (MPD), PEG 1000, PEG 3350, 1,6-HEXANEDIOL, 1- REMARK 280 BUTANOL, (RS)-1,2- PROPANEDIOL, 2-PROPANOL, 1,4-BUTANEDIOL, 1,3- REMARK 280 PROPANEDIOL, PH 6.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.81500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.82000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.77500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.82000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.81500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.77500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 GLN A 1 REMARK 465 VAL A 2 REMARK 465 LYS A 123 REMARK 465 LYS A 124 REMARK 465 LYS 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 465 HIS A 131 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 3 CG CD OE1 NE2 REMARK 470 GLN A 13 OE1 NE2 REMARK 470 SER A 25 OG REMARK 470 PHE A 27 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 43 CD CE NZ REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 ASP A 55 CG OD1 OD2 REMARK 470 ASP A 56 OD1 OD2 REMARK 470 ASN A 74 CG OD1 ND2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 LYS A 87 CD CE NZ REMARK 470 ARG A 100 NE CZ NH1 NH2 REMARK 470 LYS A 103 CD CE NZ REMARK 470 GLU A 108 CG CD OE1 OE2 REMARK 470 GLN A 114 CG CD OE1 NE2 REMARK 470 SER A 122 OG REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 201 DBREF 5IVO A 1 131 PDB 5IVO 5IVO 1 131 SEQRES 1 A 131 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 131 PRO GLY GLY SER LEU THR LEU SER CYS THR ALA SER GLY SEQRES 3 A 131 PHE THR LEU ASP HIS TYR ASP ILE GLY TRP PHE ARG GLN SEQRES 4 A 131 ALA PRO GLY LYS GLU ARG GLU GLY VAL SER CYS ILE ASN SEQRES 5 A 131 ASN SER ASP ASP ASP THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 131 GLY ARG PHE THR ILE PHE MET ASN ASN ALA LYS ASP THR SEQRES 7 A 131 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 131 ALA ILE TYR TYR CYS ALA GLU ALA ARG GLY CYS LYS ARG SEQRES 9 A 131 GLY ARG TYR GLU TYR ASP PHE TRP GLY GLN GLY THR GLN SEQRES 10 A 131 VAL THR VAL SER SER LYS LYS LYS HIS HIS HIS HIS HIS SEQRES 11 A 131 HIS HET MPD A 201 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD C6 H14 O2 FORMUL 3 HOH *40(H2 O) HELIX 1 AA1 THR A 28 TYR A 32 5 5 HELIX 2 AA2 ASP A 62 LYS A 65 5 4 HELIX 3 AA3 LYS A 87 THR A 91 5 5 HELIX 4 AA4 ARG A 100 LYS A 103 5 4 SHEET 1 AA1 4 VAL A 5 SER A 7 0 SHEET 2 AA1 4 LEU A 18 THR A 23 -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 MET A 72 -1 N PHE A 71 O TYR A 80 SHEET 1 AA2 6 GLY A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 116 VAL A 120 1 O THR A 119 N VAL A 12 SHEET 3 AA2 6 ALA A 92 GLU A 98 -1 N ALA A 92 O VAL A 118 SHEET 4 AA2 6 ILE A 34 GLN A 39 -1 N PHE A 37 O TYR A 95 SHEET 5 AA2 6 GLU A 46 ASN A 52 -1 O VAL A 48 N TRP A 36 SHEET 6 AA2 6 ASP A 57 TYR A 60 -1 O ASP A 57 N ASN A 52 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.16 SSBOND 2 CYS A 50 CYS A 102 1555 1555 2.05 SITE 1 AC1 5 PHE A 37 TYR A 60 ALA A 61 CYS A 102 SITE 2 AC1 5 LYS A 103 CRYST1 31.630 47.550 67.640 90.00 90.00 90.00 P 21 21 21 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 0.031616 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021030 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014784 0.00000