HEADER PEPTIDE BINDING PROTEIN 26-APR-22 7UTG TITLE 2D9 NANOBODY TO BCL11A-EXZF23 FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2D9-V102G NANOBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_TAXID: 30538; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BINDING PROTEIN TO BCL11A-EXZF23 FRAGMENT, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.M.K.DASSAMA,L.ZHAI REVDAT 3 25-OCT-23 7UTG 1 REMARK REVDAT 2 11-JAN-23 7UTG 1 JRNL REVDAT 1 21-DEC-22 7UTG 0 JRNL AUTH F.SHEN,G.ZHENG,M.SETEGNE,K.TENGLIN,M.IZADI,H.XIE,L.ZHAI, JRNL AUTH 2 S.H.ORKIN,L.M.K.DASSAMA JRNL TITL A CELL-PERMEANT NANOBODY-BASED DEGRADER THAT INDUCES FETAL JRNL TITL 2 HEMOGLOBIN. JRNL REF ACS CENT.SCI. V. 8 1695 2022 JRNL REFN ESSN 2374-7951 JRNL PMID 36589886 JRNL DOI 10.1021/ACSCENTSCI.2C00998 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 54642 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.820 REMARK 3 FREE R VALUE TEST SET COUNT : 3729 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 10.0000 - 3.7500 0.99 1919 143 0.1626 0.1854 REMARK 3 2 3.7500 - 2.9800 1.00 1955 134 0.1822 0.2101 REMARK 3 3 2.9800 - 2.6000 1.00 1927 148 0.2149 0.2622 REMARK 3 4 2.6000 - 2.3600 1.00 1917 151 0.2041 0.2418 REMARK 3 5 2.3600 - 2.1900 0.99 1918 142 0.1922 0.1773 REMARK 3 6 2.1900 - 2.0600 1.00 1939 142 0.1820 0.1989 REMARK 3 7 2.0600 - 1.9600 1.00 1943 136 0.1859 0.2024 REMARK 3 8 1.9600 - 1.8800 1.00 1915 145 0.1858 0.2263 REMARK 3 9 1.8800 - 1.8000 1.00 1966 140 0.1925 0.2429 REMARK 3 10 1.8000 - 1.7400 1.00 1911 146 0.1837 0.2435 REMARK 3 11 1.7400 - 1.6900 1.00 1941 142 0.2035 0.2318 REMARK 3 12 1.6900 - 1.6400 1.00 1936 141 0.2115 0.2332 REMARK 3 13 1.6400 - 1.6000 1.00 1910 142 0.2073 0.2518 REMARK 3 14 1.6000 - 1.5600 1.00 1957 141 0.1936 0.2054 REMARK 3 15 1.5600 - 1.5200 1.00 1917 138 0.1935 0.1954 REMARK 3 16 1.5200 - 1.4900 1.00 1952 153 0.2058 0.2272 REMARK 3 17 1.4900 - 1.4600 1.00 1920 141 0.1997 0.2235 REMARK 3 18 1.4600 - 1.4300 1.00 1946 142 0.2025 0.2595 REMARK 3 19 1.4300 - 1.4100 1.00 1893 139 0.2055 0.2315 REMARK 3 20 1.4100 - 1.3800 1.00 1975 155 0.2085 0.2059 REMARK 3 21 1.3800 - 1.3600 1.00 1937 133 0.2283 0.2269 REMARK 3 22 1.3600 - 1.3400 0.98 1925 127 0.2385 0.2846 REMARK 3 23 1.3400 - 1.3200 0.95 1816 145 0.2358 0.2318 REMARK 3 24 1.3200 - 1.3000 0.91 1744 125 0.2621 0.2943 REMARK 3 25 1.3000 - 1.2800 0.88 1720 138 0.2690 0.2723 REMARK 3 26 1.2800 - 1.2700 0.85 1638 106 0.2903 0.3215 REMARK 3 27 1.2700 - 1.2500 0.75 1476 94 0.3225 0.3216 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.83 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7UTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 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 : 54642 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0 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: 1NLB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1 M TRIS PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 18.30950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.37850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.12350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.37850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.30950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.12350 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 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 PRO A 126 REMARK 465 GLN A 127 REMARK 465 PHE A 128 REMARK 465 GLU A 129 REMARK 465 LYS A 130 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 NE2 GLN A 3 OE1 GLN A 13 4455 1.86 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 27 -166.51 -161.49 REMARK 500 TYR A 105 -36.62 74.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 7UTG A 1 130 PDB 7UTG 7UTG 1 130 SEQRES 1 A 130 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 130 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 130 SER ILE PHE VAL ASN ASN ALA MET GLY TRP TYR ARG GLN SEQRES 4 A 130 ALA PRO GLY LYS GLU ARG GLU LEU VAL ALA ALA ILE SER SEQRES 5 A 130 ALA SER GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 130 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 A 130 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 130 ALA VAL TYR TYR CYS ALA ALA ASP GLN ASP GLY TYR PRO SEQRES 9 A 130 TYR GLU TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 10 A 130 SER LEU GLU SER ALA TRP SER HIS PRO GLN PHE GLU LYS HET SO4 A 201 5 HET SO4 A 202 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *81(H2 O) HELIX 1 AA1 ASP A 62 LYS A 65 5 4 HELIX 2 AA2 ASN A 74 LYS A 76 5 3 HELIX 3 AA3 LYS A 87 THR A 91 5 5 HELIX 4 AA4 SER A 118 ALA A 122 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -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 SER A 71 O TYR A 80 SHEET 1 AA2 6 GLY A 10 GLN A 13 0 SHEET 2 AA2 6 THR A 112 SER A 117 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 MET A 34 GLN A 39 -1 N TYR A 37 O TYR A 95 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O ALA A 49 N TRP A 36 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O TYR A 59 N ALA A 50 SHEET 1 AA3 4 GLY A 10 GLN A 13 0 SHEET 2 AA3 4 THR A 112 SER A 117 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 GLU A 106 TRP A 108 -1 O TYR A 107 N ALA A 98 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.06 CISPEP 1 TYR A 103 PRO A 104 0 11.50 CRYST1 36.619 52.247 54.757 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 0.027308 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018263 0.00000