HEADER RNA BINDING PROTEIN 28-FEB-20 5R64 TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF HUMAN TITLE 2 CLEAVAGE FACTOR IM IN COMPLEX WITH FMOPL000464A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 5; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 25 KDA COMPND 5 SUBUNIT,CPSF 25 KDA SUBUNIT,CLEAVAGE FACTOR IM COMPLEX 25 KDA COMPND 6 SUBUNIT,CFIM25,NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 21,NUDIX COMPND 7 MOTIF 21,NUDIX HYDROLASE 21,PRE-MRNA CLEAVAGE FACTOR IM 68 KDA COMPND 8 SUBUNIT; COMPND 9 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: NUDT21, CFIM25, CPSF25, CPSF5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, NUDIX DOMAIN, KEYWDS 2 XCHEMEXPLORER, CPSF5, RNA PROCESSING, CLEAVAGE FACTOR, MRNA KEYWDS 3 PROCESSING, NUCLEUS, PHOSPHOPROTEIN, RNA-BINDING, RNA BINDING KEYWDS 4 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.TALON,T.KROJER,L.DIAZ-SAEZ,A.R.BRADLEY,A.AIMON,M.FAIRHEAD, AUTHOR 2 C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,K.V.M.HUBER,F.VON DELFT REVDAT 2 06-MAR-24 5R64 1 LINK REVDAT 1 15-APR-20 5R64 0 JRNL AUTH R.TALON,T.KROJER,L.DIAZ-SAEZ,A.R.BRADLEY,A.AIMON,M.FAIRHEAD, JRNL AUTH 2 C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,K.V.M.HUBER,F.VON DELFT JRNL TITL PANDDA ANALYSIS GROUP DEPOSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 37646 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1956 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) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2775 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3160 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -1.46000 REMARK 3 B12 (A**2) : 0.23000 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): 0.159 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.815 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3817 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3327 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4934 ; 1.800 ; 1.656 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7739 ; 1.289 ; 1.571 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 452 ; 8.096 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 189 ;33.354 ;21.852 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 603 ;15.019 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;21.057 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4157 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 788 ; 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): 1830 ; 3.720 ; 3.678 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1820 ; 3.699 ; 3.675 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2210 ; 5.230 ; 5.521 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5R64 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1001402817. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39681 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 71.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 1.92100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 3BAP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ACETATE PH 5.1, 0.0025M ZNAC, 6% REMARK 280 PEG3K, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 143.46000 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 71.73000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 71.73000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 143.46000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -214.0 KCAL/MOL 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -71.73000 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 LYS A 73 CG CD CE NZ REMARK 470 PHE A 103 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 LYS A 192 CG CD CE NZ REMARK 470 GLU B 55 CG CD OE1 OE2 REMARK 470 LYS B 56 CG CD CE NZ REMARK 470 GLU B 69 CG CD OE1 OE2 REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 ARG B 90 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 131 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 132 CG CD OE1 NE2 REMARK 470 ASP B 133 CG OD1 OD2 REMARK 470 VAL B 135 CG1 CG2 REMARK 470 LEU B 136 CG CD1 CD2 REMARK 470 GLN B 137 CG CD OE1 NE2 REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 LYS B 192 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 ZN ZN B 301 O HOH B 401 1.44 REMARK 500 OE1 GLU B 88 O HOH B 401 1.62 REMARK 500 O HOH B 504 O HOH B 509 1.79 REMARK 500 O HOH A 439 O HOH A 509 1.82 REMARK 500 OE2 GLU A 88 O HOH A 401 1.83 REMARK 500 OG1 THR A 43 O HOH A 402 1.96 REMARK 500 OE2 GLU A 88 O HOH A 403 2.02 REMARK 500 O HOH A 403 O HOH A 512 2.08 REMARK 500 O HOH B 424 O HOH B 517 2.11 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 HOH A 514 O HOH A 514 4555 0.92 REMARK 500 ZN ZN B 302 O HOH A 403 4545 1.43 REMARK 500 O HOH B 499 O HOH B 499 6554 1.73 REMARK 500 NE2 HIS A 89 O HOH B 401 3655 2.03 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 THR A 102 -123.66 -104.93 REMARK 500 PRO A 159 23.83 -78.41 REMARK 500 HIS A 164 -6.09 85.38 REMARK 500 HIS B 89 27.04 84.78 REMARK 500 ASP B 203 100.61 -49.94 REMARK 500 ASN B 204 42.39 -149.85 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 SER B 31 MET B 32 147.88 REMARK 500 THR B 101 THR B 102 -148.63 REMARK 500 TYR B 202 ASP B 203 -104.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TYR B 202 -11.07 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 B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 NE2 REMARK 620 2 HOH A 510 O 113.5 REMARK 620 3 GLU B 88 OE1 115.8 2.6 REMARK 620 4 HIS B 93 NE2 114.3 1.0 1.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HOH A 401 O 58.6 REMARK 620 3 HOH A 512 O 62.2 4.4 REMARK 620 4 HIS B 164 NE2 63.2 4.8 1.5 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue M0J A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 305 DBREF 5R64 A 33 227 UNP O43809 CPSF5_HUMAN 33 227 DBREF 5R64 B 33 227 UNP O43809 CPSF5_HUMAN 33 227 SEQADV 5R64 SER A 31 UNP O43809 EXPRESSION TAG SEQADV 5R64 MET A 32 UNP O43809 EXPRESSION TAG SEQADV 5R64 SER B 31 UNP O43809 EXPRESSION TAG SEQADV 5R64 MET B 32 UNP O43809 EXPRESSION TAG SEQRES 1 A 197 SER MET LEU GLU ARG THR ILE ASN LEU TYR PRO LEU THR SEQRES 2 A 197 ASN TYR THR PHE GLY THR LYS GLU PRO LEU TYR GLU LYS SEQRES 3 A 197 ASP SER SER VAL ALA ALA ARG PHE GLN ARG MET ARG GLU SEQRES 4 A 197 GLU PHE ASP LYS ILE GLY MET ARG ARG THR VAL GLU GLY SEQRES 5 A 197 VAL LEU ILE VAL HIS GLU HIS ARG LEU PRO HIS VAL LEU SEQRES 6 A 197 LEU LEU GLN LEU GLY THR THR PHE PHE LYS LEU PRO GLY SEQRES 7 A 197 GLY GLU LEU ASN PRO GLY GLU ASP GLU VAL GLU GLY LEU SEQRES 8 A 197 LYS ARG LEU MET THR GLU ILE LEU GLY ARG GLN ASP GLY SEQRES 9 A 197 VAL LEU GLN ASP TRP VAL ILE ASP ASP CYS ILE GLY ASN SEQRES 10 A 197 TRP TRP ARG PRO ASN PHE GLU PRO PRO GLN TYR PRO TYR SEQRES 11 A 197 ILE PRO ALA HIS ILE THR LYS PRO LYS GLU HIS LYS LYS SEQRES 12 A 197 LEU PHE LEU VAL GLN LEU GLN GLU LYS ALA LEU PHE ALA SEQRES 13 A 197 VAL PRO LYS ASN TYR LYS LEU VAL ALA ALA PRO LEU PHE SEQRES 14 A 197 GLU LEU TYR ASP ASN ALA PRO GLY TYR GLY PRO ILE ILE SEQRES 15 A 197 SER SER LEU PRO GLN LEU LEU SER ARG PHE ASN PHE ILE SEQRES 16 A 197 TYR ASN SEQRES 1 B 197 SER MET LEU GLU ARG THR ILE ASN LEU TYR PRO LEU THR SEQRES 2 B 197 ASN TYR THR PHE GLY THR LYS GLU PRO LEU TYR GLU LYS SEQRES 3 B 197 ASP SER SER VAL ALA ALA ARG PHE GLN ARG MET ARG GLU SEQRES 4 B 197 GLU PHE ASP LYS ILE GLY MET ARG ARG THR VAL GLU GLY SEQRES 5 B 197 VAL LEU ILE VAL HIS GLU HIS ARG LEU PRO HIS VAL LEU SEQRES 6 B 197 LEU LEU GLN LEU GLY THR THR PHE PHE LYS LEU PRO GLY SEQRES 7 B 197 GLY GLU LEU ASN PRO GLY GLU ASP GLU VAL GLU GLY LEU SEQRES 8 B 197 LYS ARG LEU MET THR GLU ILE LEU GLY ARG GLN ASP GLY SEQRES 9 B 197 VAL LEU GLN ASP TRP VAL ILE ASP ASP CYS ILE GLY ASN SEQRES 10 B 197 TRP TRP ARG PRO ASN PHE GLU PRO PRO GLN TYR PRO TYR SEQRES 11 B 197 ILE PRO ALA HIS ILE THR LYS PRO LYS GLU HIS LYS LYS SEQRES 12 B 197 LEU PHE LEU VAL GLN LEU GLN GLU LYS ALA LEU PHE ALA SEQRES 13 B 197 VAL PRO LYS ASN TYR LYS LEU VAL ALA ALA PRO LEU PHE SEQRES 14 B 197 GLU LEU TYR ASP ASN ALA PRO GLY TYR GLY PRO ILE ILE SEQRES 15 B 197 SER SER LEU PRO GLN LEU LEU SER ARG PHE ASN PHE ILE SEQRES 16 B 197 TYR ASN HET ZN A 301 1 HET ZN A 302 1 HET ACT A 303 4 HET ACT A 304 4 HET M0J A 305 14 HET ZN B 301 1 HET ZN B 302 1 HET ZN B 303 1 HET ZN B 304 1 HET ACT B 305 4 HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM M0J N-[(2S)-2-HYDROXYPROPYL]-N'-PHENYLUREA FORMUL 3 ZN 6(ZN 2+) FORMUL 5 ACT 3(C2 H3 O2 1-) FORMUL 7 M0J C10 H14 N2 O2 FORMUL 13 HOH *252(H2 O) HELIX 1 AA1 PRO A 41 THR A 43 5 3 HELIX 2 AA2 SER A 59 GLY A 75 1 17 HELIX 3 AA3 ASP A 116 GLY A 130 1 15 HELIX 4 AA4 LEU A 198 TYR A 202 1 5 HELIX 5 AA5 ASN A 204 SER A 213 1 10 HELIX 6 AA6 SER A 214 SER A 220 1 7 HELIX 7 AA7 PRO B 41 THR B 43 5 3 HELIX 8 AA8 SER B 59 GLY B 75 1 17 HELIX 9 AA9 ASP B 116 GLY B 130 1 15 HELIX 10 AB1 LEU B 198 TYR B 202 1 5 HELIX 11 AB2 ASN B 204 SER B 213 1 10 HELIX 12 AB3 SER B 214 SER B 220 1 7 SHEET 1 AA1 2 THR A 36 LEU A 39 0 SHEET 2 AA1 2 ASN A 223 TYR A 226 1 O ILE A 225 N LEU A 39 SHEET 1 AA2 2 TYR A 45 LYS A 50 0 SHEET 2 AA2 2 ALA A 183 PRO A 188 1 O ALA A 183 N THR A 46 SHEET 1 AA3 5 PHE A 104 LYS A 105 0 SHEET 2 AA3 5 LEU A 91 LEU A 99 -1 N LEU A 97 O LYS A 105 SHEET 3 AA3 5 ARG A 77 GLU A 88 -1 N VAL A 86 O HIS A 93 SHEET 4 AA3 5 GLU A 170 GLN A 178 1 O VAL A 177 N VAL A 83 SHEET 5 AA3 5 VAL A 140 ARG A 150 -1 N TRP A 148 O LYS A 172 SHEET 1 AA4 4 GLY A 108 GLU A 110 0 SHEET 2 AA4 4 ARG A 77 GLU A 88 -1 N VAL A 80 O GLY A 109 SHEET 3 AA4 4 LEU A 91 LEU A 99 -1 O HIS A 93 N VAL A 86 SHEET 4 AA4 4 TYR A 191 PRO A 197 -1 O VAL A 194 N LEU A 96 SHEET 1 AA5 2 THR B 36 LEU B 39 0 SHEET 2 AA5 2 ASN B 223 TYR B 226 1 O ILE B 225 N LEU B 39 SHEET 1 AA6 2 TYR B 45 LYS B 50 0 SHEET 2 AA6 2 ALA B 183 PRO B 188 1 O PHE B 185 N GLY B 48 SHEET 1 AA7 5 PHE B 103 LYS B 105 0 SHEET 2 AA7 5 PRO B 92 LEU B 99 -1 N LEU B 99 O PHE B 103 SHEET 3 AA7 5 ARG B 77 HIS B 87 -1 N LEU B 84 O LEU B 95 SHEET 4 AA7 5 GLU B 170 GLN B 178 1 O PHE B 175 N VAL B 83 SHEET 5 AA7 5 VAL B 140 ARG B 150 -1 N TRP B 148 O LYS B 172 SHEET 1 AA8 4 GLY B 108 GLU B 110 0 SHEET 2 AA8 4 ARG B 77 HIS B 87 -1 N VAL B 80 O GLY B 109 SHEET 3 AA8 4 PRO B 92 LEU B 99 -1 O LEU B 95 N LEU B 84 SHEET 4 AA8 4 LYS B 192 PRO B 197 -1 O VAL B 194 N LEU B 96 LINK ND1 HIS A 89 ZN ZN A 302 1555 1555 2.32 LINK NE2 HIS A 89 ZN ZN B 301 1555 3655 1.91 LINK NE2 HIS A 93 ZN ZN B 302 1555 4655 2.31 LINK O HOH A 401 ZN ZN B 302 4545 1555 2.29 LINK O HOH A 510 ZN ZN B 301 2544 1555 2.08 LINK O HOH A 512 ZN ZN B 302 4545 1555 2.53 LINK OE1AGLU B 88 ZN ZN B 301 1555 1555 2.12 LINK NE2 HIS B 93 ZN ZN B 301 1555 1555 2.16 LINK NE1 TRP B 149 ZN ZN B 304 1555 1555 2.20 LINK NE2 HIS B 164 ZN ZN B 302 1555 1555 1.79 CISPEP 1 GLN B 132 ASP B 133 0 -3.07 CISPEP 2 ASP B 133 GLY B 134 0 -1.78 CISPEP 3 VAL B 135 LEU B 136 0 -7.58 SITE 1 AC1 3 MET A 76 TRP A 149 HIS A 171 SITE 1 AC2 2 HIS A 89 GLU B 200 SITE 1 AC3 6 GLU A 34 ASN A 147 TRP A 149 HIS A 171 SITE 2 AC3 6 LYS A 173 HOH A 408 SITE 1 AC4 4 GLU A 200 TYR A 202 ASP A 203 ASN A 204 SITE 1 AC5 5 GLU A 81 LEU A 97 LEU A 106 GLY A 108 SITE 2 AC5 5 TYR A 191 SITE 1 AC6 6 GLU A 88 HIS A 89 HOH A 510 GLU B 88 SITE 2 AC6 6 HIS B 93 HOH B 401 SITE 1 AC7 6 GLU A 88 HIS A 93 HOH A 401 HOH A 403 SITE 2 AC7 6 HOH A 512 HIS B 164 SITE 1 AC8 4 ALA A 195 ALA A 196 HOH A 415 HOH A 420 SITE 1 AC9 2 TRP B 149 HIS B 171 SITE 1 AD1 5 HIS A 164 TYR B 160 PHE B 199 TYR B 202 SITE 2 AD1 5 HOH B 418 CRYST1 59.850 59.850 215.190 90.00 90.00 120.00 P 32 2 1 12 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 0.016708 0.009647 0.000000 0.00000 SCALE2 0.000000 0.019293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004647 0.00000