HEADER TRANSCRIPTION/DNA 11-APR-17 5XFQ TITLE TERNARY COMPLEX OF PHF1, A DNA DUPLEX AND A HISTONE PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 25-360; COMPND 5 SYNONYM: PROTEIN PHF1,POLYCOMB-LIKE PROTEIN 1,MPCL1,T-COMPLEX TESTIS- COMPND 6 EXPRESSED 3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3'); COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: PEPTIDE FROM HISTONE H3; COMPND 14 CHAIN: E, F; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PHF1, PLC1, TCTEX-3, TCTEX3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606 KEYWDS PHF1, PCL1, DNA, HISTONE, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.WANG,H.LI REVDAT 3 22-NOV-23 5XFQ 1 REMARK REVDAT 2 27-SEP-17 5XFQ 1 JRNL REVDAT 1 13-SEP-17 5XFQ 0 JRNL AUTH H.LI,R.LIEFKE,J.JIANG,J.V.KURLAND,W.TIAN,P.DENG,W.ZHANG, JRNL AUTH 2 Q.HE,D.J.PATEL,M.L.BULYK,Y.SHI,Z.WANG JRNL TITL POLYCOMB-LIKE PROTEINS LINK THE PRC2 COMPLEX TO CPG ISLANDS JRNL REF NATURE V. 549 287 2017 JRNL REFN ESSN 1476-4687 JRNL PMID 28869966 JRNL DOI 10.1038/NATURE23881 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 32405 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1648 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 47.4236 - 5.4803 0.98 2622 154 0.1778 0.2144 REMARK 3 2 5.4803 - 4.3509 0.99 2593 153 0.1838 0.2118 REMARK 3 3 4.3509 - 3.8012 0.99 2582 140 0.1873 0.2145 REMARK 3 4 3.8012 - 3.4537 1.00 2554 155 0.2204 0.2505 REMARK 3 5 3.4537 - 3.2062 0.99 2590 126 0.2537 0.3049 REMARK 3 6 3.2062 - 3.0172 0.99 2554 140 0.2707 0.3331 REMARK 3 7 3.0172 - 2.8662 0.99 2571 117 0.2790 0.2990 REMARK 3 8 2.8662 - 2.7414 0.99 2592 120 0.2769 0.3676 REMARK 3 9 2.7414 - 2.6359 0.99 2548 145 0.2827 0.3514 REMARK 3 10 2.6359 - 2.5449 0.99 2602 125 0.2959 0.3335 REMARK 3 11 2.5449 - 2.4654 0.99 2525 140 0.3046 0.3098 REMARK 3 12 2.4654 - 2.3949 0.95 2424 133 0.2984 0.3444 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.660 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 : 0.005 5724 REMARK 3 ANGLE : 0.793 7832 REMARK 3 CHIRALITY : 0.030 825 REMARK 3 PLANARITY : 0.003 913 REMARK 3 DIHEDRAL : 18.246 2173 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 5XFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-APR-17. REMARK 100 THE DEPOSITION ID IS D_1300002968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97852 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32456 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.52300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5XFN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M BIS-TRIS AT PH 6.5, 0.05M REMARK 280 AMMONIUM SULFATE, 30% PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 70.62150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.62150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.27500 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 SER A 25 REMARK 465 GLY A 26 REMARK 465 PRO A 27 REMARK 465 GLU A 340 REMARK 465 LEU A 341 REMARK 465 LEU A 342 REMARK 465 THR A 343 REMARK 465 GLY A 344 REMARK 465 ASP A 345 REMARK 465 GLY A 346 REMARK 465 ALA A 347 REMARK 465 PRO A 348 REMARK 465 THR A 349 REMARK 465 SER A 350 REMARK 465 PHE A 351 REMARK 465 PRO A 352 REMARK 465 SER A 353 REMARK 465 GLY A 354 REMARK 465 GLN A 355 REMARK 465 GLY A 356 REMARK 465 PRO A 357 REMARK 465 GLY A 358 REMARK 465 GLY A 359 REMARK 465 GLY A 360 REMARK 465 SER B 25 REMARK 465 GLY B 26 REMARK 465 PRO B 27 REMARK 465 ARG B 28 REMARK 465 PRO B 29 REMARK 465 ALA B 81 REMARK 465 ALA B 82 REMARK 465 LEU B 83 REMARK 465 PRO B 84 REMARK 465 GLY B 85 REMARK 465 GLY B 127 REMARK 465 GLU B 128 REMARK 465 GLY B 129 REMARK 465 GLU B 130 REMARK 465 GLY B 131 REMARK 465 ALA B 132 REMARK 465 LEU B 341 REMARK 465 LEU B 342 REMARK 465 THR B 343 REMARK 465 GLY B 344 REMARK 465 ASP B 345 REMARK 465 GLY B 346 REMARK 465 ALA B 347 REMARK 465 PRO B 348 REMARK 465 THR B 349 REMARK 465 SER B 350 REMARK 465 PHE B 351 REMARK 465 PRO B 352 REMARK 465 SER B 353 REMARK 465 GLY B 354 REMARK 465 GLN B 355 REMARK 465 GLY B 356 REMARK 465 PRO B 357 REMARK 465 GLY B 358 REMARK 465 GLY B 359 REMARK 465 GLY B 360 REMARK 465 DT D 13 REMARK 465 ALA E 29 REMARK 465 PRO E 30 REMARK 465 ALA E 31 REMARK 465 THR E 32 REMARK 465 GLY E 33 REMARK 465 GLY E 34 REMARK 465 ALA F 29 REMARK 465 PRO F 30 REMARK 465 ALA F 31 REMARK 465 THR F 32 REMARK 465 GLY F 33 REMARK 465 GLY F 34 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 O PRO A 337 O HOH A 501 1.99 REMARK 500 N LEU A 83 O HOH A 502 2.03 REMARK 500 O HOH A 508 O HOH A 513 2.06 REMARK 500 OE2 GLU B 66 O HOH B 501 2.07 REMARK 500 O HOH A 515 O HOH A 521 2.07 REMARK 500 O TYR E 41 O HOH E 101 2.17 REMARK 500 OG SER A 166 O HOH A 503 2.17 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 PRO B 121 C - N - CD ANGL. DEV. = 18.9 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 ASN A 102 73.77 -118.05 REMARK 500 LYS A 109 -63.47 -92.17 REMARK 500 GLU A 128 -120.69 58.09 REMARK 500 CYS A 189 -167.61 62.58 REMARK 500 GLU A 276 -55.07 -139.52 REMARK 500 ASN B 102 70.99 -116.17 REMARK 500 CYS B 189 -170.80 63.08 REMARK 500 GLU B 276 -57.95 -130.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 129 GLU A 130 -147.80 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 A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 CYS A 93 SG 109.7 REMARK 620 3 HIS A 115 ND1 102.0 97.2 REMARK 620 4 CYS A 118 SG 107.7 117.7 121.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 107 SG REMARK 620 2 CYS A 110 SG 112.8 REMARK 620 3 CYS A 136 SG 110.7 113.3 REMARK 620 4 CYS A 139 SG 110.1 96.4 112.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 189 SG REMARK 620 2 CYS A 191 SG 111.0 REMARK 620 3 HIS A 212 ND1 104.2 86.6 REMARK 620 4 CYS A 215 SG 103.9 117.7 132.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 204 SG REMARK 620 2 CYS A 207 SG 99.1 REMARK 620 3 CYS A 234 SG 108.8 117.4 REMARK 620 4 CYS A 237 SG 110.6 111.7 108.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 90 SG REMARK 620 2 CYS B 93 SG 101.2 REMARK 620 3 HIS B 115 ND1 109.4 88.2 REMARK 620 4 CYS B 118 SG 134.1 112.7 102.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 107 SG REMARK 620 2 CYS B 110 SG 104.7 REMARK 620 3 CYS B 136 SG 116.4 100.9 REMARK 620 4 CYS B 139 SG 119.1 107.0 106.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 189 SG REMARK 620 2 CYS B 191 SG 117.1 REMARK 620 3 HIS B 212 ND1 104.2 96.7 REMARK 620 4 CYS B 215 SG 100.5 120.7 117.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 204 SG REMARK 620 2 CYS B 207 SG 109.3 REMARK 620 3 CYS B 234 SG 103.4 120.3 REMARK 620 4 CYS B 237 SG 115.8 109.9 98.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XFN RELATED DB: PDB REMARK 900 RELATED ID: 5XFO RELATED DB: PDB REMARK 900 RELATED ID: 5XFP RELATED DB: PDB REMARK 900 RELATED ID: 5XFR RELATED DB: PDB DBREF 5XFQ A 25 360 UNP Q9Z1B8 PHF1_MOUSE 25 360 DBREF 5XFQ B 25 360 UNP Q9Z1B8 PHF1_MOUSE 25 360 DBREF 5XFQ C 1 13 PDB 5XFQ 5XFQ 1 13 DBREF 5XFQ D 1 13 PDB 5XFQ 5XFQ 1 13 DBREF 5XFQ E 29 41 UNP Q5TEC6 Q5TEC6_HUMAN 30 42 DBREF 5XFQ F 29 41 UNP Q5TEC6 Q5TEC6_HUMAN 30 42 SEQRES 1 A 336 SER GLY PRO ARG PRO ARG LEU TRP GLU GLY GLN ASP VAL SEQRES 2 A 336 LEU ALA ARG TRP THR ASP GLY LEU LEU TYR LEU GLY THR SEQRES 3 A 336 ILE LYS LYS VAL ASP SER ALA ARG GLU VAL CYS LEU VAL SEQRES 4 A 336 GLN PHE GLU ASP ASP SER GLN PHE LEU VAL LEU TRP LYS SEQRES 5 A 336 ASP ILE SER PRO ALA ALA LEU PRO GLY GLU GLU LEU LEU SEQRES 6 A 336 CYS CYS VAL CYS ARG SER GLU THR VAL VAL PRO GLY ASN SEQRES 7 A 336 ARG LEU VAL SER CYS GLU LYS CYS ARG HIS ALA TYR HIS SEQRES 8 A 336 GLN ASP CYS HIS VAL PRO ARG ALA PRO ALA PRO GLY GLU SEQRES 9 A 336 GLY GLU GLY ALA SER TRP VAL CYS ARG GLN CYS VAL PHE SEQRES 10 A 336 ALA ILE ALA THR LYS ARG GLY GLY ALA LEU LYS LYS GLY SEQRES 11 A 336 PRO TYR ALA ARG ALA MET LEU GLY MET LYS LEU SER LEU SEQRES 12 A 336 PRO TYR GLY LEU LYS GLY LEU ASP TRP ASP ALA GLY HIS SEQRES 13 A 336 LEU SER ASN ARG GLN GLN SER TYR CYS TYR CYS GLY GLY SEQRES 14 A 336 PRO GLY GLU TRP ASN LEU LYS MET LEU GLN CYS ARG SER SEQRES 15 A 336 CYS LEU GLN TRP PHE HIS GLU ALA CYS THR GLN CYS LEU SEQRES 16 A 336 SER LYS PRO LEU LEU TYR GLY ASP ARG PHE TYR GLU PHE SEQRES 17 A 336 GLU CYS CYS VAL CYS ARG GLY GLY PRO GLU LYS VAL ARG SEQRES 18 A 336 ARG LEU GLN LEU ARG TRP VAL ASP VAL ALA HIS LEU VAL SEQRES 19 A 336 LEU TYR HIS LEU SER VAL CYS CYS LYS LYS LYS TYR PHE SEQRES 20 A 336 ASP PHE ASP ARG GLU ILE LEU PRO PHE THR SER GLU ASN SEQRES 21 A 336 TRP ASP SER LEU LEU LEU GLY GLU LEU SER ASP THR PRO SEQRES 22 A 336 LYS GLY GLU ARG SER SER GLN LEU LEU SER ALA LEU ASN SEQRES 23 A 336 SER HIS LYS ASP ARG PHE ILE SER GLY ARG GLU ILE LYS SEQRES 24 A 336 LYS ARG LYS CYS LEU PHE GLY LEU HIS ALA ARG THR PRO SEQRES 25 A 336 PRO PRO VAL GLU LEU LEU THR GLY ASP GLY ALA PRO THR SEQRES 26 A 336 SER PHE PRO SER GLY GLN GLY PRO GLY GLY GLY SEQRES 1 B 336 SER GLY PRO ARG PRO ARG LEU TRP GLU GLY GLN ASP VAL SEQRES 2 B 336 LEU ALA ARG TRP THR ASP GLY LEU LEU TYR LEU GLY THR SEQRES 3 B 336 ILE LYS LYS VAL ASP SER ALA ARG GLU VAL CYS LEU VAL SEQRES 4 B 336 GLN PHE GLU ASP ASP SER GLN PHE LEU VAL LEU TRP LYS SEQRES 5 B 336 ASP ILE SER PRO ALA ALA LEU PRO GLY GLU GLU LEU LEU SEQRES 6 B 336 CYS CYS VAL CYS ARG SER GLU THR VAL VAL PRO GLY ASN SEQRES 7 B 336 ARG LEU VAL SER CYS GLU LYS CYS ARG HIS ALA TYR HIS SEQRES 8 B 336 GLN ASP CYS HIS VAL PRO ARG ALA PRO ALA PRO GLY GLU SEQRES 9 B 336 GLY GLU GLY ALA SER TRP VAL CYS ARG GLN CYS VAL PHE SEQRES 10 B 336 ALA ILE ALA THR LYS ARG GLY GLY ALA LEU LYS LYS GLY SEQRES 11 B 336 PRO TYR ALA ARG ALA MET LEU GLY MET LYS LEU SER LEU SEQRES 12 B 336 PRO TYR GLY LEU LYS GLY LEU ASP TRP ASP ALA GLY HIS SEQRES 13 B 336 LEU SER ASN ARG GLN GLN SER TYR CYS TYR CYS GLY GLY SEQRES 14 B 336 PRO GLY GLU TRP ASN LEU LYS MET LEU GLN CYS ARG SER SEQRES 15 B 336 CYS LEU GLN TRP PHE HIS GLU ALA CYS THR GLN CYS LEU SEQRES 16 B 336 SER LYS PRO LEU LEU TYR GLY ASP ARG PHE TYR GLU PHE SEQRES 17 B 336 GLU CYS CYS VAL CYS ARG GLY GLY PRO GLU LYS VAL ARG SEQRES 18 B 336 ARG LEU GLN LEU ARG TRP VAL ASP VAL ALA HIS LEU VAL SEQRES 19 B 336 LEU TYR HIS LEU SER VAL CYS CYS LYS LYS LYS TYR PHE SEQRES 20 B 336 ASP PHE ASP ARG GLU ILE LEU PRO PHE THR SER GLU ASN SEQRES 21 B 336 TRP ASP SER LEU LEU LEU GLY GLU LEU SER ASP THR PRO SEQRES 22 B 336 LYS GLY GLU ARG SER SER GLN LEU LEU SER ALA LEU ASN SEQRES 23 B 336 SER HIS LYS ASP ARG PHE ILE SER GLY ARG GLU ILE LYS SEQRES 24 B 336 LYS ARG LYS CYS LEU PHE GLY LEU HIS ALA ARG THR PRO SEQRES 25 B 336 PRO PRO VAL GLU LEU LEU THR GLY ASP GLY ALA PRO THR SEQRES 26 B 336 SER PHE PRO SER GLY GLN GLY PRO GLY GLY GLY SEQRES 1 C 13 DG DG DG DC DG DG DC DC DG DC DC DC DT SEQRES 1 D 13 DG DG DG DC DG DG DC DC DG DC DC DC DT SEQRES 1 E 13 ALA PRO ALA THR GLY GLY VAL M3L LYS PRO HIS ARG TYR SEQRES 1 F 13 ALA PRO ALA THR GLY GLY VAL M3L LYS PRO HIS ARG TYR MODRES 5XFQ M3L E 36 LYS MODIFIED RESIDUE MODRES 5XFQ M3L F 36 LYS MODIFIED RESIDUE HET M3L E 36 12 HET M3L F 36 12 HET ZN A 401 1 HET ZN A 402 1 HET ZN A 403 1 HET ZN A 404 1 HET ZN B 401 1 HET ZN B 402 1 HET ZN B 403 1 HET ZN B 404 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 5 M3L 2(C9 H21 N2 O2 1+) FORMUL 7 ZN 8(ZN 2+) FORMUL 15 HOH *56(H2 O) HELIX 1 AA1 ASP A 117 HIS A 119 5 3 HELIX 2 AA2 CYS A 136 THR A 145 1 10 HELIX 3 AA3 GLY A 154 LEU A 165 1 12 HELIX 4 AA4 GLY A 170 LEU A 174 5 5 HELIX 5 AA5 ALA A 214 THR A 216 5 3 HELIX 6 AA6 CYS A 234 GLY A 239 1 6 HELIX 7 AA7 ARG A 250 CYS A 266 1 17 HELIX 8 AA8 GLU A 276 ASN A 284 1 9 HELIX 9 AA9 LEU A 290 SER A 294 5 5 HELIX 10 AB1 PRO A 297 HIS A 312 1 16 HELIX 11 AB2 ARG A 320 LYS A 323 5 4 HELIX 12 AB3 CYS B 136 THR B 145 1 10 HELIX 13 AB4 GLY B 154 LYS B 164 1 11 HELIX 14 AB5 ALA B 214 THR B 216 5 3 HELIX 15 AB6 CYS B 234 GLY B 239 1 6 HELIX 16 AB7 ARG B 250 LYS B 267 1 18 HELIX 17 AB8 GLU B 276 ASN B 284 1 9 HELIX 18 AB9 LEU B 290 ASP B 295 5 6 HELIX 19 AC1 PRO B 297 HIS B 312 1 16 HELIX 20 AC2 ARG B 320 LYS B 323 5 4 SHEET 1 AA1 5 GLN A 70 LEU A 74 0 SHEET 2 AA1 5 VAL A 60 PHE A 65 -1 N VAL A 63 O PHE A 71 SHEET 3 AA1 5 LEU A 46 ASP A 55 -1 N LYS A 52 O LEU A 62 SHEET 4 AA1 5 ASP A 36 ARG A 40 -1 N VAL A 37 O GLY A 49 SHEET 5 AA1 5 ILE A 78 PRO A 80 -1 O SER A 79 N LEU A 38 SHEET 1 AA2 2 LEU A 104 SER A 106 0 SHEET 2 AA2 2 ALA A 113 HIS A 115 -1 O TYR A 114 N VAL A 105 SHEET 1 AA3 2 MET A 201 GLN A 203 0 SHEET 2 AA3 2 TRP A 210 HIS A 212 -1 O PHE A 211 N LEU A 202 SHEET 1 AA4 2 TYR A 230 GLU A 233 0 SHEET 2 AA4 2 LYS A 243 ARG A 246 -1 O ARG A 245 N GLU A 231 SHEET 1 AA5 3 PHE A 271 ASP A 272 0 SHEET 2 AA5 3 LEU A 328 LEU A 331 -1 O PHE A 329 N PHE A 271 SHEET 3 AA5 3 PHE A 316 SER A 318 -1 N ILE A 317 O GLY A 330 SHEET 1 AA6 5 GLN B 70 LEU B 74 0 SHEET 2 AA6 5 VAL B 60 PHE B 65 -1 N CYS B 61 O VAL B 73 SHEET 3 AA6 5 LEU B 46 ASP B 55 -1 N THR B 50 O GLN B 64 SHEET 4 AA6 5 ASP B 36 ARG B 40 -1 N VAL B 37 O GLY B 49 SHEET 5 AA6 5 ILE B 78 SER B 79 -1 O SER B 79 N LEU B 38 SHEET 1 AA7 2 VAL B 105 SER B 106 0 SHEET 2 AA7 2 ALA B 113 TYR B 114 -1 O TYR B 114 N VAL B 105 SHEET 1 AA8 2 MET B 201 GLN B 203 0 SHEET 2 AA8 2 TRP B 210 HIS B 212 -1 O PHE B 211 N LEU B 202 SHEET 1 AA9 2 TYR B 230 GLU B 233 0 SHEET 2 AA9 2 LYS B 243 ARG B 246 -1 O ARG B 245 N GLU B 231 SHEET 1 AB1 3 PHE B 271 ASP B 272 0 SHEET 2 AB1 3 LEU B 328 LEU B 331 -1 O PHE B 329 N PHE B 271 SHEET 3 AB1 3 PHE B 316 SER B 318 -1 N ILE B 317 O GLY B 330 LINK C VAL E 35 N M3L E 36 1555 1555 1.33 LINK C M3L E 36 N LYS E 37 1555 1555 1.33 LINK C VAL F 35 N M3L F 36 1555 1555 1.33 LINK C M3L F 36 N LYS F 37 1555 1555 1.33 LINK SG CYS A 90 ZN ZN A 401 1555 1555 2.52 LINK SG CYS A 93 ZN ZN A 401 1555 1555 2.36 LINK SG CYS A 107 ZN ZN A 402 1555 1555 2.35 LINK SG CYS A 110 ZN ZN A 402 1555 1555 2.53 LINK ND1 HIS A 115 ZN ZN A 401 1555 1555 2.12 LINK SG CYS A 118 ZN ZN A 401 1555 1555 2.29 LINK SG CYS A 136 ZN ZN A 402 1555 1555 2.45 LINK SG CYS A 139 ZN ZN A 402 1555 1555 2.43 LINK SG CYS A 189 ZN ZN A 403 1555 1555 2.47 LINK SG CYS A 191 ZN ZN A 403 1555 1555 2.44 LINK SG CYS A 204 ZN ZN A 404 1555 1555 2.39 LINK SG CYS A 207 ZN ZN A 404 1555 1555 2.33 LINK ND1 HIS A 212 ZN ZN A 403 1555 1555 2.28 LINK SG CYS A 215 ZN ZN A 403 1555 1555 2.39 LINK SG CYS A 234 ZN ZN A 404 1555 1555 2.28 LINK SG CYS A 237 ZN ZN A 404 1555 1555 2.36 LINK SG CYS B 90 ZN ZN B 403 1555 1555 2.43 LINK SG CYS B 93 ZN ZN B 403 1555 1555 2.36 LINK SG CYS B 107 ZN ZN B 404 1555 1555 2.35 LINK SG CYS B 110 ZN ZN B 404 1555 1555 2.50 LINK ND1 HIS B 115 ZN ZN B 403 1555 1555 2.34 LINK SG CYS B 118 ZN ZN B 403 1555 1555 2.88 LINK SG CYS B 136 ZN ZN B 404 1555 1555 2.59 LINK SG CYS B 139 ZN ZN B 404 1555 1555 2.47 LINK SG CYS B 189 ZN ZN B 401 1555 1555 2.42 LINK SG CYS B 191 ZN ZN B 401 1555 1555 2.34 LINK SG CYS B 204 ZN ZN B 402 1555 1555 2.42 LINK SG CYS B 207 ZN ZN B 402 1555 1555 2.32 LINK ND1 HIS B 212 ZN ZN B 401 1555 1555 2.14 LINK SG CYS B 215 ZN ZN B 401 1555 1555 2.36 LINK SG CYS B 234 ZN ZN B 402 1555 1555 2.35 LINK SG CYS B 237 ZN ZN B 402 1555 1555 2.46 CISPEP 1 VAL A 120 PRO A 121 0 -1.58 CISPEP 2 VAL B 120 PRO B 121 0 -3.11 SITE 1 AC1 4 CYS A 90 CYS A 93 HIS A 115 CYS A 118 SITE 1 AC2 4 CYS A 107 CYS A 110 CYS A 136 CYS A 139 SITE 1 AC3 4 CYS A 189 CYS A 191 HIS A 212 CYS A 215 SITE 1 AC4 4 CYS A 204 CYS A 207 CYS A 234 CYS A 237 SITE 1 AC5 4 CYS B 189 CYS B 191 HIS B 212 CYS B 215 SITE 1 AC6 4 CYS B 204 CYS B 207 CYS B 234 CYS B 237 SITE 1 AC7 4 CYS B 90 CYS B 93 HIS B 115 CYS B 118 SITE 1 AC8 4 CYS B 107 CYS B 110 CYS B 136 CYS B 139 CRYST1 141.243 62.550 97.338 90.00 103.04 90.00 C 1 2 1 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 0.007080 0.000000 0.001639 0.00000 SCALE2 0.000000 0.015987 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010545 0.00000