HEADER RNA BINDING PROTEIN 27-FEB-20 5R4Q TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF HUMAN TITLE 2 CLEAVAGE FACTOR IM IN COMPLEX WITH NM466-1 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 S.L.KIDD,N.MATEU,R.TALON,T.KROJER,A.AIMON,A.R.BRADLEY,M.FAIRHEAD, AUTHOR 2 L.DIAZ-SAEZ,H.F.SORE,A.MADIN,K.V.M.HUBER,F.VON DELFT,D.R.SPRING REVDAT 2 06-MAR-24 5R4Q 1 LINK REVDAT 1 08-JUL-20 5R4Q 0 JRNL AUTH S.L.KIDD,N.MATEU,R.TALON,T.KROJER,A.AIMON,A.R.BRADLEY, JRNL AUTH 2 M.FAIRHEAD,L.DIAZ-SAEZ,H.F.SORE,A.MADIN,K.V.M.HUBER, JRNL AUTH 3 F.VON DELFT,D.R.SPRING JRNL TITL PANDDA ANALYSIS GROUP DEPOSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.49 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 69979 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3644 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) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5091 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE SET COUNT : 260 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3142 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.55000 REMARK 3 B22 (A**2) : 0.55000 REMARK 3 B33 (A**2) : -1.77000 REMARK 3 B12 (A**2) : 0.27000 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): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.250 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 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): 4880 ; 0.010 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 3853 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5883 ; 1.840 ; 1.657 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8964 ; 1.270 ; 1.571 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 561 ;10.415 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 217 ;34.529 ;21.889 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 664 ;14.379 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.493 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 537 ; 0.224 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5087 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 943 ; 0.003 ; 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): 2422 ; 2.811 ; 3.799 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2408 ; 2.796 ; 3.795 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2707 ; 4.460 ; 5.541 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 5R4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1001402767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-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 : 73717 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 71.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.05300 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) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 1.76300 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 (%): 45.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 142.95333 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 71.47667 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 71.47667 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 142.95333 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 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 B 31 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 MET B 32 CG SD CE 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 LEU B 99 CG CD1 CD2 REMARK 470 PHE B 103 CG CD1 CD2 CE1 CE2 CZ 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 1.05 REMARK 500 OE1 GLU B 88 O HOH B 401 1.55 REMARK 500 O HOH A 401 O HOH A 521 1.99 REMARK 500 OE2 GLU A 88 O HOH A 401 2.04 REMARK 500 OE2 GLU A 88 O HOH A 402 2.06 REMARK 500 OE1 GLU A 81 O HOH A 403 2.11 REMARK 500 O HOH B 481 O HOH B 483 2.12 REMARK 500 NE2 HIS A 93 O HOH A 401 2.15 REMARK 500 O HOH A 515 O HOH A 520 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 ZN ZN B 302 O HOH A 401 4545 1.33 REMARK 500 O HOH B 495 O HOH B 495 6554 1.66 REMARK 500 NE2 HIS A 89 O HOH B 401 3655 1.85 REMARK 500 O HOH A 412 O HOH B 497 1565 2.19 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 78 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 78 NE - CZ - NH2 ANGL. DEV. = -3.3 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 THR A 102 -122.36 -99.42 REMARK 500 ILE B 74 -11.31 -143.85 REMARK 500 HIS B 89 25.79 97.25 REMARK 500 PRO B 159 34.63 -86.51 REMARK 500 ASN B 204 -107.59 -75.65 REMARK 500 ALA B 205 -53.52 108.68 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 A 31 MET A 32 148.78 REMARK 500 TYR B 202 ASP B 203 -117.72 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 406 O 114.1 REMARK 620 3 GLU B 88 OE1 116.4 2.5 REMARK 620 4 HIS B 93 NE2 114.9 0.9 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 521 O 57.1 REMARK 620 3 HIS B 164 NE2 57.9 1.4 REMARK 620 N 1 2 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 ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RW7 B 305 DBREF 5R4Q A 33 227 UNP O43809 CPSF5_HUMAN 33 227 DBREF 5R4Q B 33 227 UNP O43809 CPSF5_HUMAN 33 227 SEQADV 5R4Q SER A 31 UNP O43809 EXPRESSION TAG SEQADV 5R4Q MET A 32 UNP O43809 EXPRESSION TAG SEQADV 5R4Q SER B 31 UNP O43809 EXPRESSION TAG SEQADV 5R4Q 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 ZN B 301 1 HET ZN B 302 1 HET ZN B 303 1 HET ZN B 304 1 HET RW7 B 305 18 HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM RW7 (3S)-3,4-DIMETHYL-3-PROPYL-3,4-DIHYDRO-1H-1,4- HETNAM 2 RW7 BENZODIAZEPINE-2,5-DIONE FORMUL 3 ZN 6(ZN 2+) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 11 RW7 C14 H18 N2 O2 FORMUL 12 HOH *255(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 ASN B 204 1 7 HELIX 11 AB2 TYR B 208 SER B 213 1 6 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 PHE A 185 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 97 O LYS B 105 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 VAL B 177 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 LYS B 192 N GLN B 98 LINK ND1 HIS A 89 ZN ZN A 302 1555 1555 2.29 LINK NE2 HIS A 89 ZN ZN B 301 1555 3655 2.05 LINK NE2 HIS A 93 ZN ZN B 302 1555 4655 2.12 LINK NE1 TRP A 149 ZN ZN A 301 1555 1555 2.56 LINK O HOH A 406 ZN ZN B 301 2544 1555 1.89 LINK O HOH A 484 ZN ZN B 303 4545 1555 2.54 LINK O HOH A 521 ZN ZN B 302 4545 1555 2.47 LINK OE1 GLU B 88 ZN ZN B 301 1555 1555 2.07 LINK NE2 HIS B 93 ZN ZN B 301 1555 1555 2.03 LINK NE1 TRP B 149 ZN ZN B 304 1555 1555 2.33 LINK NE2 HIS B 164 ZN ZN B 302 1555 1555 1.85 CISPEP 1 GLN B 132 ASP B 133 0 -12.32 CISPEP 2 ASP B 133 GLY B 134 0 2.28 CISPEP 3 VAL B 135 LEU B 136 0 2.84 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 7 GLU A 34 ASN A 147 HIS A 171 LYS A 173 SITE 2 AC3 7 PHE A 222 HOH A 405 HOH A 409 SITE 1 AC4 4 PHE A 199 TYR A 202 ASP A 203 ASN A 204 SITE 1 AC5 5 HIS A 89 HOH A 406 GLU B 88 HIS B 93 SITE 2 AC5 5 HOH B 401 SITE 1 AC6 6 GLU A 88 HIS A 93 HOH A 401 HOH A 402 SITE 2 AC6 6 HOH A 521 HIS B 164 SITE 1 AC7 4 ALA A 195 ALA A 196 GLU A 200 HOH A 484 SITE 1 AC8 2 TRP B 149 HIS B 171 SITE 1 AC9 6 LEU B 53 GLY B 108 GLY B 109 ILE B 128 SITE 2 AC9 6 TYR B 191 HOH B 434 CRYST1 59.680 59.680 214.430 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 0.016756 0.009674 0.000000 0.00000 SCALE2 0.000000 0.019348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004664 0.00000