HEADER DNA BINDING PROTEIN 07-JAN-21 7BGF TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DIMERIC COILED COIL OF THE HUMAN TITLE 2 CTIP PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA ENDONUCLEASE RBBP8,CTIP/RBBP8; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CTBP-INTERACTING PROTEIN,CTIP,RETINOBLASTOMA-BINDING PROTEIN COMPND 5 8,RBBP-8,RETINOBLASTOMA-INTERACTING PROTEIN AND MYOSIN-LIKE,RIM, COMPND 6 SPORULATION IN THE ABSENCE OF SPO11 PROTEIN 2 HOMOLOG,SAE2; COMPND 7 EC: 3.1.-.-; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: THE CONSTRUCT EXPRESSES AMINO ACIDS 31 TO 145 OF HUMAN COMPND 10 CTIP. IT CONTAINS TWO SINGLE-POINT MUTATIONS: C89 AND C92 HAVE BEEN COMPND 11 MUTATED TO ALANINE. THE GSMG PEPTIDE AT THE N-TERMINUS CONTAINS THE COMPND 12 AMINO ACIDS LEFT OVER AFTER TEV CLEAVAGE OF THE MBP TAG, AND IS NOT COMPND 13 PART OF THE CTIP SEQUENCE. THE WSHPQFEK SEQUENCE AT THE C-TERMINUS COMPND 14 REPRESENTS THE STREP TAG PEPTIDE AND IS NOT PART OF THE CTIP COMPND 15 SEQUENCE.,THE CONSTRUCT EXPRESSES AMINO ACIDS 31 TO 145 OF HUMAN COMPND 16 CTIP. IT CONTAINS TWO SINGLE-POINT MUTATIONS: C89 AND C92 HAVE BEEN COMPND 17 MUTATED TO ALANINE. THE GSMG PEPTIDE AT THE N-TERMINUS CONTAINS THE COMPND 18 AMINO ACIDS LEFT OVER AFTER TEV CLEAVAGE OF THE MBP TAG, AND IS NOT COMPND 19 PART OF THE CTIP SEQUENCE. THE WSHPQFEK SEQUENCE AT THE C-TERMINUS COMPND 20 REPRESENTS THE STREP TAG PEPTIDE AND IS NOT PART OF THE CTIP COMPND 21 SEQUENCE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RBBP8, CTIP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 KEYWDS COILED COIL, DIMER, DNA REPAIR, HOMOLOGOUS RECOMBINATION, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.R.MORTON,L.PELLEGRINI REVDAT 2 01-MAY-24 7BGF 1 REMARK REVDAT 1 30-JUN-21 7BGF 0 JRNL AUTH C.R.MORTON,N.J.RZECHORZEK,J.D.MAMAN,M.KURAMOCHI,H.SEKIGUCHI, JRNL AUTH 2 R.RAMBO,Y.C.SASAKI,O.R.DAVIES,L.PELLEGRINI JRNL TITL STRUCTURAL BASIS FOR THE COILED-COIL ARCHITECTURE OF HUMAN JRNL TITL 2 CTIP. JRNL REF OPEN BIOLOGY V. 11 10060 2021 JRNL REFN ESSN 2046-2441 JRNL PMID 34129781 JRNL DOI 10.1098/RSOB.210060 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 8612 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 79.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 101.8 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 7BGF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292113239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976251 REMARK 200 MONOCHROMATOR : NULL 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8624 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.802 REMARK 200 RESOLUTION RANGE LOW (A) : 37.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05463 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.75810 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.290 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: HOMOLOGY MODELS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CONDITION F6 OF THE MORPHEUS REMARK 280 CRYSTALLISATION SCREEN MD-47 (MOLECULAR DIMENSIONS)., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.40067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.20033 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 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 GLY A 27 REMARK 465 SER A 28 REMARK 465 MET A 29 REMARK 465 ILE A 142 REMARK 465 GLU A 143 REMARK 465 ASN A 144 REMARK 465 ASP A 145 REMARK 465 TRP A 146 REMARK 465 SER A 147 REMARK 465 HIS A 148 REMARK 465 PRO A 149 REMARK 465 GLN A 150 REMARK 465 PHE A 151 REMARK 465 GLU A 152 REMARK 465 LYS A 153 REMARK 465 GLY B 27 REMARK 465 SER B 28 REMARK 465 MET B 29 REMARK 465 GLY B 30 REMARK 465 GLN B 139 REMARK 465 GLN B 140 REMARK 465 LYS B 141 REMARK 465 ILE B 142 REMARK 465 GLU B 143 REMARK 465 ASN B 144 REMARK 465 ASP B 145 REMARK 465 TRP B 146 REMARK 465 SER B 147 REMARK 465 HIS B 148 REMARK 465 PRO B 149 REMARK 465 GLN B 150 REMARK 465 PHE B 151 REMARK 465 GLU B 152 REMARK 465 LYS B 153 DBREF 7BGF A 31 145 UNP Q99708 CTIP_HUMAN 31 145 DBREF 7BGF A 146 153 PDB 7BGF 7BGF 146 153 DBREF 7BGF B 31 145 UNP Q99708 CTIP_HUMAN 31 145 DBREF 7BGF B 146 153 PDB 7BGF 7BGF 146 153 SEQADV 7BGF GLY A 27 UNP Q99708 EXPRESSION TAG SEQADV 7BGF SER A 28 UNP Q99708 EXPRESSION TAG SEQADV 7BGF MET A 29 UNP Q99708 EXPRESSION TAG SEQADV 7BGF GLY A 30 UNP Q99708 EXPRESSION TAG SEQADV 7BGF ALA A 89 UNP Q99708 CYS 89 ENGINEERED MUTATION SEQADV 7BGF ALA A 92 UNP Q99708 CYS 92 ENGINEERED MUTATION SEQADV 7BGF GLY B 27 UNP Q99708 EXPRESSION TAG SEQADV 7BGF SER B 28 UNP Q99708 EXPRESSION TAG SEQADV 7BGF MET B 29 UNP Q99708 EXPRESSION TAG SEQADV 7BGF GLY B 30 UNP Q99708 EXPRESSION TAG SEQADV 7BGF ALA B 89 UNP Q99708 CYS 89 ENGINEERED MUTATION SEQADV 7BGF ALA B 92 UNP Q99708 CYS 92 ENGINEERED MUTATION SEQRES 1 A 127 GLY SER MET GLY HIS ASP ARG GLU VAL GLN GLY LEU GLN SEQRES 2 A 127 VAL LYS VAL THR LYS LEU LYS GLN GLU ARG ILE LEU ASP SEQRES 3 A 127 ALA GLN ARG LEU GLU GLU PHE PHE THR LYS ASN GLN GLN SEQRES 4 A 127 LEU ARG GLU GLN GLN LYS VAL LEU HIS GLU THR ILE LYS SEQRES 5 A 127 VAL LEU GLU ASP ARG LEU ARG ALA GLY LEU ALA ASP ARG SEQRES 6 A 127 ALA ALA VAL THR GLU GLU HIS MET ARG LYS LYS GLN GLN SEQRES 7 A 127 GLU PHE GLU ASN ILE ARG GLN GLN ASN LEU LYS LEU ILE SEQRES 8 A 127 THR GLU LEU MET ASN GLU ARG ASN THR LEU GLN GLU GLU SEQRES 9 A 127 ASN LYS LYS LEU SER GLU GLN LEU GLN GLN LYS ILE GLU SEQRES 10 A 127 ASN ASP TRP SER HIS PRO GLN PHE GLU LYS SEQRES 1 B 127 GLY SER MET GLY HIS ASP ARG GLU VAL GLN GLY LEU GLN SEQRES 2 B 127 VAL LYS VAL THR LYS LEU LYS GLN GLU ARG ILE LEU ASP SEQRES 3 B 127 ALA GLN ARG LEU GLU GLU PHE PHE THR LYS ASN GLN GLN SEQRES 4 B 127 LEU ARG GLU GLN GLN LYS VAL LEU HIS GLU THR ILE LYS SEQRES 5 B 127 VAL LEU GLU ASP ARG LEU ARG ALA GLY LEU ALA ASP ARG SEQRES 6 B 127 ALA ALA VAL THR GLU GLU HIS MET ARG LYS LYS GLN GLN SEQRES 7 B 127 GLU PHE GLU ASN ILE ARG GLN GLN ASN LEU LYS LEU ILE SEQRES 8 B 127 THR GLU LEU MET ASN GLU ARG ASN THR LEU GLN GLU GLU SEQRES 9 B 127 ASN LYS LYS LEU SER GLU GLN LEU GLN GLN LYS ILE GLU SEQRES 10 B 127 ASN ASP TRP SER HIS PRO GLN PHE GLU LYS FORMUL 3 HOH *36(H2 O) HELIX 1 AA1 GLY A 30 LYS A 141 1 112 HELIX 2 AA2 ASP B 32 LEU B 138 1 107 CRYST1 86.598 86.598 42.601 90.00 90.00 120.00 P 32 6 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 0.011548 0.006667 0.000000 0.00000 SCALE2 0.000000 0.013334 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023474 0.00000