HEADER TRANSCRIPTION 10-AUG-16 5SYB TITLE CRYSTAL STRUCTURE OF HUMAN PHF5A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER-LIKE DOMAIN-CONTAINING PROTEIN 5A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHD FINGER-LIKE DOMAIN PROTEIN 5A, SPLICING FACTOR 3B- COMPND 5 ASSOCIATED 14 KDA PROTEIN, SF3B14B, P14B, RDS3 HOMOLOG; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PHF5A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21*; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CORE COMPONENT, SF3B COMPLEX, HUMAN SPLICEOSOME, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.H.C.TSAI,T.TENG,P.ZHU,P.FEKKES,N.A.LARSEN REVDAT 4 06-MAR-24 5SYB 1 REMARK REVDAT 3 07-JUN-17 5SYB 1 JRNL REVDAT 2 26-OCT-16 5SYB 1 COMPND REVDAT 1 07-SEP-16 5SYB 0 JRNL AUTH T.TENG,J.H.TSAI,X.PUYANG,M.SEILER,S.PENG,S.PRAJAPATI,D.AIRD, JRNL AUTH 2 S.BUONAMICI,B.CALEB,B.CHAN,L.CORSON,J.FEALA,P.FEKKES, JRNL AUTH 3 B.GERARD,C.KARR,M.KORPAL,X.LIU,J.T LOWE,Y.MIZUI,J.PALACINO, JRNL AUTH 4 E.PARK,P.G.SMITH,V.SUBRAMANIAN,Z.J.WU,J.ZOU,L.YU,A.CHICAS, JRNL AUTH 5 M.WARMUTH,N.LARSEN,P.ZHU JRNL TITL SPLICING MODULATORS ACT AT THE BRANCH POINT ADENOSINE JRNL TITL 2 BINDING POCKET DEFINED BY THE PHF5A-SF3B COMPLEX. JRNL REF NAT COMMUN V. 8 15522 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28541300 JRNL DOI 10.1038/NCOMMS15522 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16010 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 876 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1139 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1364 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.770 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1398 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1322 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1872 ; 1.981 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3060 ; 1.183 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 178 ; 7.428 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 60 ;34.711 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 242 ;16.379 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.022 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 200 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1580 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 304 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 718 ; 3.253 ; 2.973 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 717 ; 3.249 ; 2.969 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 894 ; 4.656 ; 4.420 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 895 ; 4.656 ; 4.428 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 680 ; 5.155 ; 3.738 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 680 ; 5.152 ; 3.738 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 979 ; 7.948 ; 5.373 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1643 ; 9.672 ;25.561 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1644 ; 9.669 ;25.566 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5SYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 318806 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 58.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM CHES PH9.5 0.8MM SODIUM CITRATE REMARK 280 0.5% BETA-OG, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+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 41.05800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.05800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.05800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.05800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.05800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.05800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 41.05800 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 41.05800 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 41.05800 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 41.05800 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 41.05800 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 41.05800 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 41.05800 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 41.05800 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 41.05800 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 41.05800 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 41.05800 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 41.05800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 349 LIES ON A SPECIAL POSITION. 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 -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY A 92 REMARK 465 SER A 93 REMARK 465 SER A 94 REMARK 465 LYS A 95 REMARK 465 THR A 96 REMARK 465 ASP A 97 REMARK 465 LEU A 98 REMARK 465 PHE A 99 REMARK 465 TYR A 100 REMARK 465 GLU A 101 REMARK 465 ARG A 102 REMARK 465 LYS A 103 REMARK 465 LYS A 104 REMARK 465 TYR A 105 REMARK 465 GLY A 106 REMARK 465 PHE A 107 REMARK 465 LYS A 108 REMARK 465 LYS A 109 REMARK 465 ARG A 110 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 93 REMARK 465 SER B 94 REMARK 465 LYS B 95 REMARK 465 THR B 96 REMARK 465 ASP B 97 REMARK 465 LEU B 98 REMARK 465 PHE B 99 REMARK 465 TYR B 100 REMARK 465 GLU B 101 REMARK 465 ARG B 102 REMARK 465 LYS B 103 REMARK 465 LYS B 104 REMARK 465 TYR B 105 REMARK 465 GLY B 106 REMARK 465 PHE B 107 REMARK 465 LYS B 108 REMARK 465 LYS B 109 REMARK 465 ARG B 110 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 91 CG CD1 CD2 REMARK 470 LYS B 3 CG CD CE NZ 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 CE LYS A 3 O HIS A 5 1.65 REMARK 500 O HOH A 301 O HOH B 339 2.15 REMARK 500 O HOH A 312 O HOH A 335 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 O HIS A 4 NH2 ARG A 57 8544 1.96 REMARK 500 O HOH A 303 O HOH A 303 7555 2.11 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 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 38 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 38 NE - CZ - NH2 ANGL. DEV. = -3.5 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 HIS A 4 -89.58 63.85 REMARK 500 ARG A 12 16.63 47.89 REMARK 500 HIS B 4 -54.07 -138.98 REMARK 500 ASP B 7 -6.25 -143.61 REMARK 500 SER B 40 -48.38 -131.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 349 DISTANCE = 6.55 ANGSTROMS 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 CYS A 46 SG 102.8 REMARK 620 3 CYS A 49 SG 112.2 102.0 REMARK 620 4 CYS A 85 SG 114.0 115.8 109.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 CYS A 26 SG 102.7 REMARK 620 3 CYS A 58 SG 110.8 106.7 REMARK 620 4 CYS A 61 SG 102.5 118.0 115.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 30 SG REMARK 620 2 CYS A 33 SG 108.4 REMARK 620 3 CYS A 72 SG 112.1 104.7 REMARK 620 4 CYS A 75 SG 107.3 112.0 112.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 11 SG REMARK 620 2 CYS B 46 SG 108.8 REMARK 620 3 CYS B 49 SG 112.0 102.5 REMARK 620 4 CYS B 85 SG 108.3 115.7 109.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 23 SG REMARK 620 2 CYS B 26 SG 104.7 REMARK 620 3 CYS B 58 SG 114.5 107.3 REMARK 620 4 CYS B 61 SG 100.5 117.3 112.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 30 SG REMARK 620 2 CYS B 33 SG 108.2 REMARK 620 3 CYS B 72 SG 113.2 103.8 REMARK 620 4 CYS B 75 SG 107.3 112.7 111.8 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 205 DBREF 5SYB A 1 110 UNP Q7RTV0 PHF5A_HUMAN 1 110 DBREF 5SYB B 1 110 UNP Q7RTV0 PHF5A_HUMAN 1 110 SEQADV 5SYB GLY A -2 UNP Q7RTV0 EXPRESSION TAG SEQADV 5SYB GLY A -1 UNP Q7RTV0 EXPRESSION TAG SEQADV 5SYB HIS A 0 UNP Q7RTV0 EXPRESSION TAG SEQADV 5SYB SER A 40 UNP Q7RTV0 CYS 40 ENGINEERED MUTATION SEQADV 5SYB GLY B -2 UNP Q7RTV0 EXPRESSION TAG SEQADV 5SYB GLY B -1 UNP Q7RTV0 EXPRESSION TAG SEQADV 5SYB HIS B 0 UNP Q7RTV0 EXPRESSION TAG SEQADV 5SYB SER B 40 UNP Q7RTV0 CYS 40 ENGINEERED MUTATION SEQRES 1 A 113 GLY GLY HIS MET ALA LYS HIS HIS PRO ASP LEU ILE PHE SEQRES 2 A 113 CYS ARG LYS GLN ALA GLY VAL ALA ILE GLY ARG LEU CYS SEQRES 3 A 113 GLU LYS CYS ASP GLY LYS CYS VAL ILE CYS ASP SER TYR SEQRES 4 A 113 VAL ARG PRO SER THR LEU VAL ARG ILE CYS ASP GLU CYS SEQRES 5 A 113 ASN TYR GLY SER TYR GLN GLY ARG CYS VAL ILE CYS GLY SEQRES 6 A 113 GLY PRO GLY VAL SER ASP ALA TYR TYR CYS LYS GLU CYS SEQRES 7 A 113 THR ILE GLN GLU LYS ASP ARG ASP GLY CYS PRO LYS ILE SEQRES 8 A 113 VAL ASN LEU GLY SER SER LYS THR ASP LEU PHE TYR GLU SEQRES 9 A 113 ARG LYS LYS TYR GLY PHE LYS LYS ARG SEQRES 1 B 113 GLY GLY HIS MET ALA LYS HIS HIS PRO ASP LEU ILE PHE SEQRES 2 B 113 CYS ARG LYS GLN ALA GLY VAL ALA ILE GLY ARG LEU CYS SEQRES 3 B 113 GLU LYS CYS ASP GLY LYS CYS VAL ILE CYS ASP SER TYR SEQRES 4 B 113 VAL ARG PRO SER THR LEU VAL ARG ILE CYS ASP GLU CYS SEQRES 5 B 113 ASN TYR GLY SER TYR GLN GLY ARG CYS VAL ILE CYS GLY SEQRES 6 B 113 GLY PRO GLY VAL SER ASP ALA TYR TYR CYS LYS GLU CYS SEQRES 7 B 113 THR ILE GLN GLU LYS ASP ARG ASP GLY CYS PRO LYS ILE SEQRES 8 B 113 VAL ASN LEU GLY SER SER LYS THR ASP LEU PHE TYR GLU SEQRES 9 B 113 ARG LYS LYS TYR GLY PHE LYS LYS ARG HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET EDO A 204 4 HET EDO A 205 4 HET ZN B 201 1 HET ZN B 202 1 HET ZN B 203 1 HET EDO B 204 4 HET EDO B 205 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 6(ZN 2+) FORMUL 6 EDO 4(C2 H6 O2) FORMUL 13 HOH *97(H2 O) HELIX 1 AA1 CYS A 46 TYR A 51 1 6 HELIX 2 AA2 LYS A 73 GLN A 78 1 6 HELIX 3 AA3 GLU A 79 GLY A 84 5 6 HELIX 4 AA4 TYR B 51 GLN B 55 5 5 HELIX 5 AA5 LYS B 73 GLN B 78 1 6 HELIX 6 AA6 GLU B 79 GLY B 84 5 6 SHEET 1 AA1 2 LEU A 8 PHE A 10 0 SHEET 2 AA1 2 ILE A 88 ASN A 90 -1 O VAL A 89 N ILE A 9 SHEET 1 AA2 2 ALA A 18 ILE A 19 0 SHEET 2 AA2 2 ARG A 44 ILE A 45 -1 O ILE A 45 N ALA A 18 SHEET 1 AA3 2 ARG A 21 LEU A 22 0 SHEET 2 AA3 2 SER A 67 ASP A 68 -1 O SER A 67 N LEU A 22 SHEET 1 AA4 2 PRO A 39 LEU A 42 0 SHEET 2 AA4 2 TYR A 70 CYS A 72 -1 O TYR A 71 N SER A 40 SHEET 1 AA5 2 LEU B 8 PHE B 10 0 SHEET 2 AA5 2 ILE B 88 ASN B 90 -1 O VAL B 89 N ILE B 9 SHEET 1 AA6 2 ALA B 18 ILE B 19 0 SHEET 2 AA6 2 ARG B 44 ILE B 45 -1 O ILE B 45 N ALA B 18 SHEET 1 AA7 2 ARG B 21 LEU B 22 0 SHEET 2 AA7 2 SER B 67 ASP B 68 -1 O SER B 67 N LEU B 22 SHEET 1 AA8 2 PRO B 39 LEU B 42 0 SHEET 2 AA8 2 TYR B 70 CYS B 72 -1 O TYR B 71 N SER B 40 LINK SG CYS A 11 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 23 ZN ZN A 203 1555 1555 2.29 LINK SG CYS A 26 ZN ZN A 203 1555 1555 2.32 LINK SG CYS A 30 ZN ZN A 202 1555 1555 2.33 LINK SG CYS A 33 ZN ZN A 202 1555 1555 2.36 LINK SG CYS A 46 ZN ZN A 201 1555 1555 2.37 LINK SG CYS A 49 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 58 ZN ZN A 203 1555 1555 2.38 LINK SG CYS A 61 ZN ZN A 203 1555 1555 2.30 LINK SG CYS A 72 ZN ZN A 202 1555 1555 2.35 LINK SG CYS A 75 ZN ZN A 202 1555 1555 2.28 LINK SG CYS A 85 ZN ZN A 201 1555 1555 2.35 LINK SG CYS B 11 ZN ZN B 201 1555 1555 2.37 LINK SG CYS B 23 ZN ZN B 203 1555 1555 2.31 LINK SG CYS B 26 ZN ZN B 203 1555 1555 2.34 LINK SG CYS B 30 ZN ZN B 202 1555 1555 2.32 LINK SG CYS B 33 ZN ZN B 202 1555 1555 2.40 LINK SG CYS B 46 ZN ZN B 201 1555 1555 2.32 LINK SG CYS B 49 ZN ZN B 201 1555 1555 2.37 LINK SG CYS B 58 ZN ZN B 203 1555 1555 2.42 LINK SG CYS B 61 ZN ZN B 203 1555 1555 2.41 LINK SG CYS B 72 ZN ZN B 202 1555 1555 2.27 LINK SG CYS B 75 ZN ZN B 202 1555 1555 2.33 LINK SG CYS B 85 ZN ZN B 201 1555 1555 2.39 CISPEP 1 LYS A 3 HIS A 4 0 -0.25 SITE 1 AC1 4 CYS A 11 CYS A 46 CYS A 49 CYS A 85 SITE 1 AC2 4 CYS A 30 CYS A 33 CYS A 72 CYS A 75 SITE 1 AC3 4 CYS A 23 CYS A 26 CYS A 58 CYS A 61 SITE 1 AC4 4 GLY A 16 VAL A 17 ASP A 47 HOH A 309 SITE 1 AC5 5 PHE A 10 ARG A 12 LYS A 80 ASP A 83 SITE 2 AC5 5 HOH A 302 SITE 1 AC6 4 CYS B 11 CYS B 46 CYS B 49 CYS B 85 SITE 1 AC7 4 CYS B 30 CYS B 33 CYS B 72 CYS B 75 SITE 1 AC8 4 CYS B 23 CYS B 26 CYS B 58 CYS B 61 SITE 1 AC9 5 PHE B 10 ARG B 12 LYS B 80 ASP B 83 SITE 2 AC9 5 HOH B 301 SITE 1 AD1 3 GLY B 16 VAL B 17 ASP B 47 CRYST1 82.116 82.116 82.116 90.00 90.00 90.00 P 21 3 24 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 0.012178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012178 0.00000