HEADER TRANSCRIPTION 27-OCT-15 5EGO TITLE HOXB13-MEIS1 HETERODIMER BOUND TO METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN MEIS1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 279-333; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*(5CM) COMPND 8 P*GP*AP*GP*G)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*CP*CP*TP*(5CM) COMPND 13 P*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3'); COMPND 14 CHAIN: E; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: HOMEOBOX PROTEIN HOX-B13; COMPND 18 CHAIN: B; COMPND 19 FRAGMENT: UNP RESIDUES 217-277; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MEIS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETG20A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 GENE: HOXB13; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 25 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 26 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 27 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 28 EXPRESSION_SYSTEM_PLASMID: PETG20A KEYWDS TRANSCRIPTION FACTOR, HETERODIMER, COMPLEX, BOUND TO DNA, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.MORGUNOVA,Y.YIN,A.JOLMA,A.POPOV,J.TAIPALE REVDAT 3 10-JAN-24 5EGO 1 REMARK REVDAT 2 17-MAY-17 5EGO 1 JRNL REVDAT 1 09-NOV-16 5EGO 0 JRNL AUTH Y.YIN,E.MORGUNOVA,A.JOLMA,E.KAASINEN,B.SAHU,S.KHUND-SAYEED, JRNL AUTH 2 P.K.DAS,T.KIVIOJA,K.DAVE,F.ZHONG,K.R.NITTA,M.TAIPALE, JRNL AUTH 3 A.POPOV,P.A.GINNO,S.DOMCKE,J.YAN,D.SCHUBELER,C.VINSON, JRNL AUTH 4 J.TAIPALE JRNL TITL IMPACT OF CYTOSINE METHYLATION ON DNA BINDING SPECIFICITIES JRNL TITL 2 OF HUMAN TRANSCRIPTION FACTORS. JRNL REF SCIENCE V. 356 2017 JRNL REFN ESSN 1095-9203 JRNL PMID 28473536 JRNL DOI 10.1126/SCIENCE.AAJ2239 REMARK 2 REMARK 2 RESOLUTION. 2.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 8214 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 379 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 2.9076 - 2.5401 0.98 2555 130 0.3921 0.4971 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.10 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 1855 REMARK 3 ANGLE : 1.065 2644 REMARK 3 CHIRALITY : 0.040 290 REMARK 3 PLANARITY : 0.005 209 REMARK 3 DIHEDRAL : 27.895 746 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 5EGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214881. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.984000 REMARK 200 MONOCHROMATOR : SI(111) AND SI (311) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8290 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.76100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 4XRM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000, POTASSIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE, TRIS, PEG 400, PH 8, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 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 20.48800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.78750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.74000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.78750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.48800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.74000 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: 6770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E, 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 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 OE2 GLU B 232 NH1 ARG B 267 1.76 REMARK 500 OP2 DG D 23 O HOH D 101 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC D 25 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG D 36 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG D 37 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA E 8 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA E 17 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES 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 LYS B 219 135.61 -34.01 REMARK 500 LEU B 275 83.89 -65.61 REMARK 500 ALA B 276 74.79 -176.12 REMARK 500 LYS B 277 120.55 64.94 REMARK 500 REMARK 500 REMARK: NULL DBREF 5EGO A 279 333 UNP O00470 MEIS1_HUMAN 279 333 DBREF 5EGO D 20 37 PDB 5EGO 5EGO 20 37 DBREF 5EGO E 1 18 PDB 5EGO 5EGO 1 18 DBREF 5EGO B 217 277 UNP Q92826 HXB13_HUMAN 217 277 SEQADV 5EGO ALA A 278 UNP O00470 EXPRESSION TAG SEQADV 5EGO MET A 334 UNP O00470 EXPRESSION TAG SEQADV 5EGO VAL B 278 UNP Q92826 EXPRESSION TAG SEQADV 5EGO LYS B 279 UNP Q92826 EXPRESSION TAG SEQRES 1 A 57 ALA PHE PRO LYS VAL ALA THR ASN ILE MET ARG ALA TRP SEQRES 2 A 57 LEU PHE GLN HIS LEU THR HIS PRO TYR PRO SER GLU GLU SEQRES 3 A 57 GLN LYS LYS GLN LEU ALA GLN ASP THR GLY LEU THR ILE SEQRES 4 A 57 LEU GLN VAL ASN ASN TRP PHE ILE ASN ALA ARG ARG ARG SEQRES 5 A 57 ILE VAL GLN PRO MET SEQRES 1 D 18 DG DT DT DG DA DC DA DG DT DT DT DT DA SEQRES 2 D 18 5CM DG DA DG DG SEQRES 1 E 18 DC DC DT 5CM DG DT DA DA DA DA DC DT DG SEQRES 2 E 18 DT DC DA DA DC SEQRES 1 B 63 ARG LYS LYS ARG ILE PRO TYR SER LYS GLY GLN LEU ARG SEQRES 2 B 63 GLU LEU GLU ARG GLU TYR ALA ALA ASN LYS PHE ILE THR SEQRES 3 B 63 LYS ASP LYS ARG ARG LYS ILE SER ALA ALA THR SER LEU SEQRES 4 B 63 SER GLU ARG GLN ILE THR ILE TRP PHE GLN ASN ARG ARG SEQRES 5 B 63 VAL LYS GLU LYS LYS VAL LEU ALA LYS VAL LYS HET 5CM D 33 20 HET 5CM E 4 20 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 5 HOH *20(H2 O) HELIX 1 AA1 PRO A 280 HIS A 294 1 15 HELIX 2 AA2 SER A 301 GLY A 313 1 13 HELIX 3 AA3 THR A 315 ILE A 330 1 16 HELIX 4 AA4 SER B 224 ALA B 236 1 13 HELIX 5 AA5 THR B 242 SER B 254 1 13 HELIX 6 AA6 SER B 256 LYS B 273 1 18 LINK O3' DA D 32 P 5CM D 33 1555 1555 1.54 LINK O3' 5CM D 33 P DG D 34 1555 1555 1.60 LINK O3' DT E 3 P 5CM E 4 1555 1555 1.60 LINK O3' 5CM E 4 P DG E 5 1555 1555 1.60 CISPEP 1 ALA B 276 LYS B 277 0 18.25 CRYST1 40.976 51.480 113.575 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 0.024405 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008805 0.00000