HEADER RNA BINDING PROTEIN 27-MAR-20 6YGU TITLE CRYSTAL STRUCTURE OF THE MINIMAL MTR4-RED1 COMPLEX (SINGLE CHAIN) FROM TITLE 2 CHAETOMIUM THERMOPHILUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP DEPENDENT RNA HELICASE (DOB1)-LIKE PROTEIN; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RED1; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM; SOURCE 3 ORGANISM_TAXID: 209285; SOURCE 4 GENE: CTHT_0001850; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24D; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM; SOURCE 12 ORGANISM_TAXID: 209285; SOURCE 13 GENE: CTHT_0014920; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET24D KEYWDS NCRNA DEGRADATION, MTREC, NUCLEAR EXOSOME, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.DOBREV,Y.L.AHMED,I.SINNING REVDAT 2 23-JUN-21 6YGU 1 JRNL REVDAT 1 05-MAY-21 6YGU 0 JRNL AUTH N.DOBREV,Y.L.AHMED,A.SIVADAS,K.SONI,T.FISCHER,I.SINNING JRNL TITL THE ZINC-FINGER PROTEIN RED1 ORCHESTRATES MTREC SUBMODULES JRNL TITL 2 AND BINDS THE MTL1 HELICASE ARCH DOMAIN. JRNL REF NAT COMMUN V. 12 3456 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34103492 JRNL DOI 10.1038/S41467-021-23565-3 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 89392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 4511 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 47.4712 - 6.1790 1.00 2821 159 0.1631 0.2175 REMARK 3 2 6.1790 - 4.9061 1.00 2842 132 0.1755 0.2498 REMARK 3 3 4.9061 - 4.2864 1.00 2877 134 0.1547 0.2123 REMARK 3 4 4.2864 - 3.8947 1.00 2832 139 0.1640 0.1709 REMARK 3 5 3.8947 - 3.6156 1.00 2846 148 0.1845 0.1983 REMARK 3 6 3.6156 - 3.4025 1.00 2813 144 0.2047 0.2153 REMARK 3 7 3.4025 - 3.2322 1.00 2815 130 0.2267 0.2420 REMARK 3 8 3.2322 - 3.0915 1.00 2867 162 0.2190 0.2577 REMARK 3 9 3.0915 - 2.9725 1.00 2794 161 0.2240 0.2909 REMARK 3 10 2.9725 - 2.8700 1.00 2855 141 0.2196 0.2379 REMARK 3 11 2.8700 - 2.7802 1.00 2810 171 0.2268 0.2820 REMARK 3 12 2.7802 - 2.7008 1.00 2838 129 0.2286 0.3108 REMARK 3 13 2.7008 - 2.6297 1.00 2802 161 0.2268 0.3008 REMARK 3 14 2.6297 - 2.5655 1.00 2869 150 0.2229 0.2978 REMARK 3 15 2.5655 - 2.5072 1.00 2789 151 0.2174 0.2910 REMARK 3 16 2.5072 - 2.4538 1.00 2881 150 0.2293 0.2699 REMARK 3 17 2.4538 - 2.4048 1.00 2829 169 0.2363 0.2921 REMARK 3 18 2.4048 - 2.3594 1.00 2760 166 0.2384 0.3168 REMARK 3 19 2.3594 - 2.3172 1.00 2895 118 0.2441 0.3129 REMARK 3 20 2.3172 - 2.2780 1.00 2798 159 0.2448 0.2579 REMARK 3 21 2.2780 - 2.2412 1.00 2812 164 0.2442 0.3920 REMARK 3 22 2.2412 - 2.2067 1.00 2858 155 0.2580 0.3237 REMARK 3 23 2.2067 - 2.1743 1.00 2842 123 0.2496 0.2904 REMARK 3 24 2.1743 - 2.1437 1.00 2784 148 0.2685 0.3293 REMARK 3 25 2.1437 - 2.1147 1.00 2833 175 0.2855 0.4022 REMARK 3 26 2.1147 - 2.0872 1.00 2829 171 0.2869 0.3614 REMARK 3 27 2.0872 - 2.0611 1.00 2803 142 0.3096 0.3978 REMARK 3 28 2.0611 - 2.0363 1.00 2795 163 0.3186 0.3772 REMARK 3 29 2.0363 - 2.0126 1.00 2873 133 0.3308 0.3521 REMARK 3 30 2.0126 - 1.9900 1.00 2819 163 0.3408 0.4026 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.87 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 : 0.013 4633 REMARK 3 ANGLE : 1.317 6255 REMARK 3 CHIRALITY : 0.069 660 REMARK 3 PLANARITY : 0.009 826 REMARK 3 DIHEDRAL : 11.117 3263 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 10.3685 15.5537 107.7067 REMARK 3 T TENSOR REMARK 3 T11: 0.2245 T22: 0.3152 REMARK 3 T33: 0.2878 T12: -0.0358 REMARK 3 T13: -0.0123 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 0.3009 L22: 1.0142 REMARK 3 L33: 0.5757 L12: -0.2976 REMARK 3 L13: 0.1033 L23: -0.1945 REMARK 3 S TENSOR REMARK 3 S11: 0.0114 S12: -0.0913 S13: -0.0287 REMARK 3 S21: 0.0048 S22: 0.0364 S23: 0.0648 REMARK 3 S31: 0.0174 S32: -0.0658 S33: 0.0005 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 6YGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292100870. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2741 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47338 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 47.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.10330 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 1.33200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.550 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 (%): 49.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE 20% PEG 3350, REMARK 280 PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 22.48950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.18350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.45300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 84.18350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.48950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.45300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 MET A 653 REMARK 465 SER A 865 REMARK 465 GLY A 866 REMARK 465 GLY A 867 REMARK 465 SER A 868 REMARK 465 GLY A 869 REMARK 465 GLY A 870 REMARK 465 SER A 871 REMARK 465 ALA B 1014 REMARK 465 LEU B 1015 REMARK 465 SER B 1016 REMARK 465 ASP B 1083 REMARK 465 GLU B 1084 REMARK 465 ARG B 1085 REMARK 465 ILE B 1086 REMARK 465 LEU B 1087 REMARK 465 LEU B 1088 REMARK 465 GLU B 1089 REMARK 465 LEU B 1090 REMARK 465 SER B 1091 REMARK 465 GLY B 1092 REMARK 465 SER B 1093 REMARK 465 HIS B 1094 REMARK 465 HIS B 1095 REMARK 465 HIS B 1096 REMARK 465 HIS B 1097 REMARK 465 HIS B 1098 REMARK 465 HIS B 1099 REMARK 465 SER C 868 REMARK 465 GLY C 869 REMARK 465 GLY C 870 REMARK 465 SER C 871 REMARK 465 ALA D 1014 REMARK 465 LEU D 1015 REMARK 465 SER D 1016 REMARK 465 ALA D 1082 REMARK 465 ASP D 1083 REMARK 465 GLU D 1084 REMARK 465 ARG D 1085 REMARK 465 ILE D 1086 REMARK 465 LEU D 1087 REMARK 465 LEU D 1088 REMARK 465 GLU D 1089 REMARK 465 LEU D 1090 REMARK 465 SER D 1091 REMARK 465 GLY D 1092 REMARK 465 SER D 1093 REMARK 465 HIS D 1094 REMARK 465 HIS D 1095 REMARK 465 HIS D 1096 REMARK 465 HIS D 1097 REMARK 465 HIS D 1098 REMARK 465 HIS D 1099 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 NZ LYS A 814 O HOH A 1001 1.75 REMARK 500 NE ARG B 1035 O HOH B 1201 2.06 REMARK 500 OD1 ASP C 840 O HOH C 1001 2.08 REMARK 500 NH2 ARG A 665 O HOH A 1002 2.14 REMARK 500 NH2 ARG D 1025 O TYR D 1046 2.14 REMARK 500 OE1 GLN A 820 O1 EDO A 905 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 SG CYS B 1066 O HOH B 1201 4556 2.15 REMARK 500 NH2 ARG B 1035 O THR B 1064 4456 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG D1025 CG ARG D1025 CD -0.230 REMARK 500 CYS D1066 CB CYS D1066 SG -0.130 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 720 CG - CD - NE ANGL. DEV. = -20.2 DEGREES REMARK 500 ARG A 720 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 720 NE - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG D1025 CA - CB - CG ANGL. DEV. = -23.2 DEGREES REMARK 500 ARG D1025 CG - CD - NE ANGL. DEV. = -16.9 DEGREES REMARK 500 ARG D1025 NE - CZ - NH1 ANGL. DEV. = -4.4 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 ARG A 720 -83.81 -11.98 REMARK 500 SER A 799 -138.84 -93.20 REMARK 500 ASP A 840 135.55 -39.79 REMARK 500 PRO C 795 98.44 -63.74 REMARK 500 SER C 802 -140.79 55.72 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 GLU A 719 ARG A 720 142.64 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 B1103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1057 SG REMARK 620 2 CYS B1066 SG 106.0 REMARK 620 3 CYS B1070 SG 111.3 124.5 REMARK 620 4 HIS B1074 NE2 103.7 96.8 112.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D1057 SG REMARK 620 2 CYS D1066 SG 101.6 REMARK 620 3 CYS D1070 SG 115.6 121.0 REMARK 620 4 HIS D1074 NE2 111.8 104.2 102.3 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 ACT A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 1101 DBREF 6YGU A 654 865 UNP G0RZ64 G0RZ64_CHATD 654 865 DBREF 6YGU B 1014 1091 UNP G0S1V1 G0S1V1_CHATD 1032 1108 DBREF 6YGU C 654 865 UNP G0RZ64 G0RZ64_CHATD 654 865 DBREF 6YGU D 1014 1091 UNP G0S1V1 G0S1V1_CHATD 1032 1108 SEQADV 6YGU MET A 653 UNP G0RZ64 INITIATING METHIONINE SEQADV 6YGU GLY A 866 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU GLY A 867 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU SER A 868 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU GLY A 869 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU GLY A 870 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU SER A 871 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU ALA B 1081 UNP G0S1V1 INSERTION SEQADV 6YGU GLY B 1092 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU SER B 1093 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS B 1094 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS B 1095 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS B 1096 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS B 1097 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS B 1098 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS B 1099 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU MET C 653 UNP G0RZ64 INITIATING METHIONINE SEQADV 6YGU GLY C 866 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU GLY C 867 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU SER C 868 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU GLY C 869 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU GLY C 870 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU SER C 871 UNP G0RZ64 EXPRESSION TAG SEQADV 6YGU ALA D 1081 UNP G0S1V1 INSERTION SEQADV 6YGU GLY D 1092 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU SER D 1093 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS D 1094 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS D 1095 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS D 1096 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS D 1097 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS D 1098 UNP G0S1V1 EXPRESSION TAG SEQADV 6YGU HIS D 1099 UNP G0S1V1 EXPRESSION TAG SEQRES 1 A 219 MET ASP GLU ALA LEU ILE LYS ASP TYR HIS SER ILE ARG SEQRES 2 A 219 GLU GLN ILE ASP GLN TYR THR LYS ASP MET VAL LEU VAL SEQRES 3 A 219 MET GLN HIS PRO THR ASN CYS VAL LYS TYR ILE ASN PRO SEQRES 4 A 219 GLY ARG LEU MET HIS VAL VAL THR SER ASP GLY THR ASP SEQRES 5 A 219 PHE GLY TRP GLY VAL ILE ILE ASN PHE TYR GLU ARG ARG SEQRES 6 A 219 PRO GLU ARG ASN ASN PRO ASN PRO GLY TRP SER PRO GLN SEQRES 7 A 219 GLU SER TYR VAL VAL GLU VAL LEU LEU ARG LEU SER SER SEQRES 8 A 219 ASP SER GLY SER VAL ASP SER LYS LEU LYS ASP ASN GLN SEQRES 9 A 219 CYS ILE PRO ALA GLY ILE ALA PRO VAL THR GLN LYS ASN SEQRES 10 A 219 ASP PRO GLY ARG TRP GLU VAL VAL PRO CYS LEU LEU SER SEQRES 11 A 219 CYS MET HIS GLY LEU SER GLN ILE LYS LEU HIS VAL PRO SEQRES 12 A 219 ASP LYS LYS SER GLY GLY SER MET ASP ASP PRO GLU THR SEQRES 13 A 219 ARG ARG ARG VAL GLY LYS SER LEU LEU GLU VAL GLN ARG SEQRES 14 A 219 ARG PHE GLU ASP GLY ILE PRO HIS MET ASP PRO ILE GLU SEQRES 15 A 219 ASN MET HIS ILE ARG ASP VAL GLU PHE LYS LYS LEU LEU SEQRES 16 A 219 ARG LYS ILE GLU VAL LEU GLU SER ARG LEU VAL ALA ASN SEQRES 17 A 219 PRO LEU HIS ASN SER GLY GLY SER GLY GLY SER SEQRES 1 B 86 ALA LEU SER TYR SER SER PRO LEU ARG PHE PHE ARG ASN SEQRES 2 B 86 PHE ARG PHE HIS PRO GLU PHE THR ARG LEU VAL ALA GLY SEQRES 3 B 86 GLY TRP ARG SER LEU THR TYR SER SER ARG ILE ASP PRO SEQRES 4 B 86 ASP LYS GLU MET CYS PRO TYR GLU LEU GLU GLY THR GLN SEQRES 5 B 86 CYS PRO SER GLY CYS SER PHE GLN HIS PHE VAL ASP ILE SEQRES 6 B 86 THR PRO ALA ALA ASP GLU ARG ILE LEU LEU GLU LEU SER SEQRES 7 B 86 GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 C 219 MET ASP GLU ALA LEU ILE LYS ASP TYR HIS SER ILE ARG SEQRES 2 C 219 GLU GLN ILE ASP GLN TYR THR LYS ASP MET VAL LEU VAL SEQRES 3 C 219 MET GLN HIS PRO THR ASN CYS VAL LYS TYR ILE ASN PRO SEQRES 4 C 219 GLY ARG LEU MET HIS VAL VAL THR SER ASP GLY THR ASP SEQRES 5 C 219 PHE GLY TRP GLY VAL ILE ILE ASN PHE TYR GLU ARG ARG SEQRES 6 C 219 PRO GLU ARG ASN ASN PRO ASN PRO GLY TRP SER PRO GLN SEQRES 7 C 219 GLU SER TYR VAL VAL GLU VAL LEU LEU ARG LEU SER SER SEQRES 8 C 219 ASP SER GLY SER VAL ASP SER LYS LEU LYS ASP ASN GLN SEQRES 9 C 219 CYS ILE PRO ALA GLY ILE ALA PRO VAL THR GLN LYS ASN SEQRES 10 C 219 ASP PRO GLY ARG TRP GLU VAL VAL PRO CYS LEU LEU SER SEQRES 11 C 219 CYS MET HIS GLY LEU SER GLN ILE LYS LEU HIS VAL PRO SEQRES 12 C 219 ASP LYS LYS SER GLY GLY SER MET ASP ASP PRO GLU THR SEQRES 13 C 219 ARG ARG ARG VAL GLY LYS SER LEU LEU GLU VAL GLN ARG SEQRES 14 C 219 ARG PHE GLU ASP GLY ILE PRO HIS MET ASP PRO ILE GLU SEQRES 15 C 219 ASN MET HIS ILE ARG ASP VAL GLU PHE LYS LYS LEU LEU SEQRES 16 C 219 ARG LYS ILE GLU VAL LEU GLU SER ARG LEU VAL ALA ASN SEQRES 17 C 219 PRO LEU HIS ASN SER GLY GLY SER GLY GLY SER SEQRES 1 D 86 ALA LEU SER TYR SER SER PRO LEU ARG PHE PHE ARG ASN SEQRES 2 D 86 PHE ARG PHE HIS PRO GLU PHE THR ARG LEU VAL ALA GLY SEQRES 3 D 86 GLY TRP ARG SER LEU THR TYR SER SER ARG ILE ASP PRO SEQRES 4 D 86 ASP LYS GLU MET CYS PRO TYR GLU LEU GLU GLY THR GLN SEQRES 5 D 86 CYS PRO SER GLY CYS SER PHE GLN HIS PHE VAL ASP ILE SEQRES 6 D 86 THR PRO ALA ALA ASP GLU ARG ILE LEU LEU GLU LEU SER SEQRES 7 D 86 GLY SER HIS HIS HIS HIS HIS HIS HET ACT A 901 4 HET EDO A 902 4 HET EDO A 903 4 HET EDO A 904 4 HET EDO A 905 4 HET EDO A 906 4 HET EDO A 907 4 HET ACT B1101 4 HET EDO B1102 4 HET ZN B1103 1 HET EDO C 901 4 HET ZN D1101 1 HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 6 EDO 8(C2 H6 O2) FORMUL 14 ZN 2(ZN 2+) FORMUL 17 HOH *180(H2 O) HELIX 1 AA1 GLU A 655 HIS A 681 1 27 HELIX 2 AA2 HIS A 681 VAL A 686 1 6 HELIX 3 AA3 LYS A 687 ILE A 689 5 3 HELIX 4 AA4 SER A 728 GLU A 731 5 4 HELIX 5 AA5 ASP A 805 PHE A 823 1 19 HELIX 6 AA6 ASP A 840 ASN A 860 1 21 HELIX 7 AA7 PHE B 1024 HIS B 1030 5 7 HELIX 8 AA8 GLU B 1032 VAL B 1037 1 6 HELIX 9 AA9 GLY B 1039 SER B 1047 5 9 HELIX 10 AB1 CYS B 1057 GLY B 1063 1 7 HELIX 11 AB2 HIS B 1074 THR B 1079 1 6 HELIX 12 AB3 GLU C 655 HIS C 681 1 27 HELIX 13 AB4 HIS C 681 VAL C 686 1 6 HELIX 14 AB5 LYS C 687 ILE C 689 5 3 HELIX 15 AB6 SER C 728 GLU C 731 5 4 HELIX 16 AB7 GLY C 801 ASP C 804 5 4 HELIX 17 AB8 ASP C 805 PHE C 823 1 19 HELIX 18 AB9 ASP C 840 ASN C 860 1 21 HELIX 19 AC1 PHE D 1024 HIS D 1030 5 7 HELIX 20 AC2 GLU D 1032 VAL D 1037 1 6 HELIX 21 AC3 GLY D 1039 SER D 1043 5 5 HELIX 22 AC4 CYS D 1057 GLU D 1062 1 6 HELIX 23 AC5 HIS D 1074 THR D 1079 1 6 SHEET 1 AA1 5 ARG A 773 LEU A 780 0 SHEET 2 AA1 5 TYR A 733 LEU A 741 -1 N VAL A 735 O CYS A 779 SHEET 3 AA1 5 ASP A 704 GLU A 715 -1 N VAL A 709 O LEU A 738 SHEET 4 AA1 5 ARG A 693 VAL A 698 -1 N ARG A 693 O ILE A 710 SHEET 5 AA1 5 MET A 784 LYS A 791 -1 O HIS A 785 N HIS A 696 SHEET 1 AA2 6 ARG C 773 LEU C 780 0 SHEET 2 AA2 6 TYR C 733 LEU C 741 -1 N VAL C 735 O CYS C 779 SHEET 3 AA2 6 ASP C 704 GLU C 715 -1 N ILE C 711 O GLU C 736 SHEET 4 AA2 6 ARG C 693 VAL C 698 -1 N MET C 695 O GLY C 708 SHEET 5 AA2 6 MET C 784 LEU C 792 -1 O HIS C 785 N HIS C 696 SHEET 6 AA2 6 GLU D1055 MET D1056 1 O MET D1056 N LYS C 791 LINK SG CYS B1057 ZN ZN B1103 1555 1555 2.44 LINK SG CYS B1066 ZN ZN B1103 1555 1555 2.21 LINK SG CYS B1070 ZN ZN B1103 1555 1555 2.30 LINK NE2 HIS B1074 ZN ZN B1103 1555 1555 2.08 LINK SG CYS D1057 ZN ZN D1101 1555 1555 2.30 LINK SG CYS D1066 ZN ZN D1101 1555 1555 2.36 LINK SG CYS D1070 ZN ZN D1101 1555 1555 2.27 LINK NE2 HIS D1074 ZN ZN D1101 1555 1555 2.04 SITE 1 AC1 4 GLY A 706 TRP A 707 ARG A 740 GLN A 820 SITE 1 AC2 1 GLU A 824 SITE 1 AC3 4 GLY A 726 GLU A 731 HOH A1038 GLU C 824 SITE 1 AC4 5 HIS A 793 VAL A 794 ASP A 796 HOH A1010 SITE 2 AC4 5 GLU B1055 SITE 1 AC5 6 TRP A 707 GLN A 820 GLY A 826 ILE A 827 SITE 2 AC5 6 HOH A1020 HOH A1045 SITE 1 AC6 6 TYR A 714 GLU A 715 ARG A 717 HOH A1007 SITE 2 AC6 6 GLY D1069 HOH D1203 SITE 1 AC7 3 TYR A 733 HOH A1003 SER D1071 SITE 1 AC8 4 LYS A 687 TYR A 688 ASN A 690 ASP B1053 SITE 1 AC9 6 LYS B1054 CYS B1070 PHE B1072 HIS B1074 SITE 2 AC9 6 ASP B1077 HOH B1218 SITE 1 AD1 4 CYS B1057 CYS B1066 CYS B1070 HIS B1074 SITE 1 AD2 5 TRP C 707 ARG C 740 TRP C 774 GLN C 820 SITE 2 AD2 5 HOH C1010 SITE 1 AD3 4 CYS D1057 CYS D1066 CYS D1070 HIS D1074 CRYST1 44.979 88.906 168.367 90.00 90.00 90.00 P 21 21 21 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 0.022233 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011248 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005939 0.00000