HEADER DNA BINDING PROTEIN 26-JUL-22 8DTU TITLE THE COMPLEX OF NANOBODY 5344N74D WITH BCL11A ZF6. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY 5344N74D; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NANOBODY 5344N74D; COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: B-CELL LYMPHOMA/LEUKEMIA 11A; COMPND 11 CHAIN: C; COMPND 12 SYNONYM: BCL-11A,B-CELL CLL/LYMPHOMA 11A,COUP-TF-INTERACTING PROTEIN COMPND 13 1,ECOTROPIC VIRAL INTEGRATION SITE 9 PROTEIN HOMOLOG,EVI-9,ZINC COMPND 14 FINGER PROTEIN 856, ZF6; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 8 ORGANISM_TAXID: 9844; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: BCL11A, CTIP1, EVI9, KIAA1809, ZNF856; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOBODY, BCL11A, TRANSCRIPTION FACTOR, ZINC FINGER DOMAIN, PROTEIN KEYWDS 2 DEGRADATION, GAMMA GLOBIN, SICKLE CELLS, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.YIN,K.TENGLIN,L.ZHAI,L.M.DASSAMA,S.H.ORKIN REVDAT 1 01-FEB-23 8DTU 0 JRNL AUTH M.YIN,M.IZADI,K.TENGLIN,T.VIENNET,L.ZHAI,G.ZHENG, JRNL AUTH 2 H.ARTHANARI,L.M.K.DASSAMA,S.H.ORKIN JRNL TITL EVOLUTION OF NANOBODIES SPECIFIC FOR BCL11A. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 59120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 36626555 JRNL DOI 10.1073/PNAS.2218959120 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 10390 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.264 REMARK 3 R VALUE (WORKING SET) : 0.261 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1011 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 40.6600 - 4.6791 1.00 1456 164 0.2285 0.2782 REMARK 3 2 4.6791 - 3.7147 1.00 1346 150 0.2216 0.2192 REMARK 3 3 3.7147 - 3.2454 0.99 1315 147 0.2692 0.2853 REMARK 3 4 3.2454 - 2.9488 0.98 1304 143 0.3172 0.3607 REMARK 3 5 2.9488 - 2.7375 0.96 1226 138 0.3369 0.3637 REMARK 3 6 2.7375 - 2.5761 0.93 1218 129 0.3682 0.4225 REMARK 3 7 2.5761 - 2.4471 0.91 1168 140 0.3825 0.3758 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.57 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 : 0.012 1159 REMARK 3 ANGLE : 1.318 1563 REMARK 3 CHIRALITY : 0.057 167 REMARK 3 PLANARITY : 0.005 197 REMARK 3 DIHEDRAL : 23.302 417 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 8DTU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267357. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10390 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.447 REMARK 200 RESOLUTION RANGE LOW (A) : 40.664 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 35.00 REMARK 200 R MERGE (I) : 0.15470 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 36.20 REMARK 200 R MERGE FOR SHELL (I) : 2.12300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.770 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5-8.2, 2.2M LI2SO4., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 78.66400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.75350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.75350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 117.99600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.75350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.75350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.33200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.75350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.75350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 117.99600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.75350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.75350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.33200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.66400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C 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 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 SG CYS A 22 SG CYS A 96 1.72 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 VAL B 2 -70.09 -140.58 REMARK 500 ALA A 14 150.34 -49.91 REMARK 500 TYR C 812 36.72 -89.24 REMARK 500 SER C 813 114.33 -168.47 REMARK 500 SER C 824 -147.37 -103.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 802 SG REMARK 620 2 CYS C 805 SG 102.0 REMARK 620 3 HIS C 818 NE2 104.2 86.3 REMARK 620 4 HIS C 823 NE2 129.3 116.4 109.7 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8DTN RELATED DB: PDB DBREF 8DTU B 1 6 PDB 8DTU 8DTU 1 6 DBREF 8DTU A 7 119 PDB 8DTU 8DTU 7 119 DBREF 8DTU C 799 826 UNP Q9H165 BC11A_HUMAN 799 826 SEQRES 1 B 6 GLN VAL GLN LEU VAL LYS SEQRES 1 A 113 SER GLY GLY GLY LEU VAL GLN ALA GLY ASP SER LEU ARG SEQRES 2 A 113 LEU SER CYS ALA ALA SER GLY SER THR PHE SER GLY TYR SEQRES 3 A 113 ALA MSE GLY TRP TYR ARG GLN ALA PRO GLY LYS GLU ARG SEQRES 4 A 113 GLU LEU VAL ALA ALA ILE THR SER SER GLY ALA SER THR SEQRES 5 A 113 TYR TYR ALA ASP SER VAL ARG GLY ARG PHE THR ILE SER SEQRES 6 A 113 ARG ASP ASP ALA LYS ASN THR VAL TYR LEU GLN MSE ASN SEQRES 7 A 113 SER LEU LYS PRO GLU ASP THR ALA VAL TYR TYR CYS ALA SEQRES 8 A 113 ALA LEU ASP GLU GLY TYR LEU ASP TYR ASP SER TRP GLY SEQRES 9 A 113 GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 C 28 VAL TYR LYS CYS GLU ILE CYS LYS MET PRO PHE SER VAL SEQRES 2 C 28 TYR SER THR LEU GLU LYS HIS MET LYS LYS TRP HIS SER SEQRES 3 C 28 ASP ARG HET MSE A 34 8 HET MSE A 83 8 HET ZN C 901 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION FORMUL 2 MSE 2(C5 H11 N O2 SE) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *17(H2 O) HELIX 1 AA1 ASP A 62 ARG A 65 5 4 HELIX 2 AA2 ASP A 74 LYS A 76 5 3 HELIX 3 AA3 LYS A 87 THR A 91 5 5 HELIX 4 AA4 ASP A 100 GLY A 102 5 3 HELIX 5 AA5 ASP A 105 TRP A 109 5 5 HELIX 6 AA6 THR C 814 SER C 824 1 11 SHEET 1 AA1 4 GLN B 3 VAL B 5 0 SHEET 2 AA1 4 LEU A 18 ALA A 23 -1 O SER A 21 N VAL B 5 SHEET 3 AA1 4 THR A 78 MSE A 83 -1 O MSE 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 LEU A 11 VAL A 12 0 SHEET 2 AA2 6 THR A 113 VAL A 117 1 O THR A 116 N VAL A 12 SHEET 3 AA2 6 ALA A 92 ALA A 98 -1 N TYR A 94 O THR A 113 SHEET 4 AA2 6 MSE 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 VAL A 48 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 2 TYR C 800 LYS C 801 0 SHEET 2 AA3 2 PRO C 808 PHE C 809 -1 O PHE C 809 N TYR C 800 LINK C ALA A 33 N MSE A 34 1555 1555 1.33 LINK C MSE A 34 N GLY A 35 1555 1555 1.33 LINK C GLN A 82 N MSE A 83 1555 1555 1.33 LINK C MSE A 83 N ASN A 84 1555 1555 1.33 LINK SG CYS C 802 ZN ZN C 901 1555 1555 2.51 LINK SG CYS C 805 ZN ZN C 901 1555 1555 2.09 LINK NE2 HIS C 818 ZN ZN C 901 1555 1555 2.04 LINK NE2 HIS C 823 ZN ZN C 901 1555 1555 2.07 CRYST1 57.507 57.507 157.328 90.00 90.00 90.00 P 43 21 2 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 0.017389 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006356 0.00000