HEADER HYDROLASE 26-JUN-21 7R8K TITLE CRYSTAL STRUCTURE OF PSEUDOOCEANICOLA LIPOLYTICUS ARGONAUTE (SEMET TITLE 2 LABELED PROTEIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGONAUTE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOOCEANICOLA LIPOLYTICUS; SOURCE 3 ORGANISM_TAXID: 2029104; SOURCE 4 GENE: CVM52_05730; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ARGONAUTE, AGO, DNA GUIDE, RNA CLEAVAGE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHIN,K.S.MURAKAMI REVDAT 2 28-DEC-22 7R8K 1 JRNL REVDAT 1 06-JUL-22 7R8K 0 JRNL AUTH L.LISITSKAYA,Y.SHIN,A.AGAPOV,A.OLINA,E.KROPOCHEVA, JRNL AUTH 2 S.RYAZANSKY,A.A.ARAVIN,D.ESYUNINA,K.S.MURAKAMI, JRNL AUTH 3 A.KULBACHINSKIY JRNL TITL PROGRAMMABLE RNA TARGETING BY BACTERIAL ARGONAUTE NUCLEASES JRNL TITL 2 WITH UNCONVENTIONAL GUIDE BINDING AND CLEAVAGE SPECIFICITY. JRNL REF NAT COMMUN V. 13 4624 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35941106 JRNL DOI 10.1038/S41467-022-32079-5 REMARK 2 REMARK 2 RESOLUTION. 3.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 19786 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.750 REMARK 3 FREE R VALUE TEST SET COUNT : 1930 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 47.1000 - 7.9100 1.00 1379 152 0.1549 0.1861 REMARK 3 2 7.9000 - 6.2700 1.00 1339 150 0.2407 0.2867 REMARK 3 3 6.2700 - 5.4800 1.00 1332 139 0.2411 0.3204 REMARK 3 4 5.4800 - 4.9800 1.00 1308 144 0.2260 0.3009 REMARK 3 5 4.9800 - 4.6300 0.99 1306 138 0.2148 0.2594 REMARK 3 6 4.6200 - 4.3500 0.98 1287 137 0.2066 0.2552 REMARK 3 7 4.3500 - 4.1400 0.98 1282 144 0.2289 0.2347 REMARK 3 8 4.1300 - 3.9600 0.97 1258 139 0.2255 0.2944 REMARK 3 9 3.9500 - 3.8000 0.97 1275 135 0.2536 0.2951 REMARK 3 10 3.8000 - 3.6700 0.97 1244 132 0.2734 0.3411 REMARK 3 11 3.6700 - 3.5600 0.95 1244 132 0.2851 0.3326 REMARK 3 12 3.5600 - 3.4600 0.94 1220 136 0.3221 0.3856 REMARK 3 13 3.4500 - 3.3600 0.92 1205 134 0.3496 0.4164 REMARK 3 14 3.3600 - 3.2800 0.89 1177 118 0.3734 0.3883 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) : 0.494 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 127.8 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 6164 REMARK 3 ANGLE : 1.702 8337 REMARK 3 CHIRALITY : 0.075 909 REMARK 3 PLANARITY : 0.014 1093 REMARK 3 DIHEDRAL : 9.267 843 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7R8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257720. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9717 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19786 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.280 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL PH 8.0, 8% PEG 8000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 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 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 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 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 99.90650 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 99.90650 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 99.90650 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 99.90650 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 99.90650 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 99.90650 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 99.90650 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 99.90650 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 99.90650 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 99.90650 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 99.90650 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 99.90650 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 99.90650 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 99.90650 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 99.90650 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 99.90650 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 99.90650 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 99.90650 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 99.90650 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 99.90650 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 99.90650 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 99.90650 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 99.90650 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 99.90650 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 99.90650 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 99.90650 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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 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 ASP A 767 REMARK 465 ASP A 768 REMARK 465 ALA A 769 REMARK 465 ALA A 770 REMARK 465 GLU A 771 REMARK 465 TYR A 772 REMARK 465 ASP A 773 REMARK 465 VAL A 774 REMARK 465 ASP A 775 REMARK 465 VAL A 776 REMARK 465 VAL A 777 REMARK 465 ARG A 778 REMARK 465 PHE A 779 REMARK 465 ALA A 780 REMARK 465 ASP A 781 REMARK 465 GLY A 782 REMARK 465 ASN A 783 REMARK 465 THR A 784 REMARK 465 GLY A 785 REMARK 465 GLU A 786 REMARK 465 ALA A 787 REMARK 465 SER A 788 REMARK 465 ALA A 789 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 ARG A 110 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 766 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ALA A 327 N ALA A 329 2.10 REMARK 500 OH TYR A 436 OE1 GLU A 449 2.16 REMARK 500 OG SER A 19 N LEU A 97 2.18 REMARK 500 NZ LYS A 358 OE2 GLU A 366 2.19 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 CYS A 704 CB CYS A 704 SG -0.117 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 LEU A 28 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 LEU A 31 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LEU A 109 CB - CG - CD2 ANGL. DEV. = -15.2 DEGREES REMARK 500 LEU A 550 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 CYS A 751 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 LEU A 765 CA - CB - CG ANGL. DEV. = 13.8 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 6 42.52 -108.53 REMARK 500 LEU A 16 33.77 -141.90 REMARK 500 ALA A 18 50.09 -146.63 REMARK 500 TYR A 20 -3.57 61.12 REMARK 500 GLU A 33 -4.27 66.05 REMARK 500 THR A 34 -20.68 -141.61 REMARK 500 TYR A 36 -33.81 -39.24 REMARK 500 LEU A 58 46.95 -144.00 REMARK 500 ASP A 61 -106.91 69.32 REMARK 500 TYR A 71 -1.34 -140.39 REMARK 500 VAL A 72 -87.29 58.76 REMARK 500 PHE A 75 62.51 63.05 REMARK 500 ARG A 80 48.07 38.34 REMARK 500 VAL A 89 107.79 -58.42 REMARK 500 TYR A 106 45.29 -85.14 REMARK 500 PRO A 136 170.84 -55.19 REMARK 500 LEU A 146 84.23 60.20 REMARK 500 ASP A 147 124.56 -24.28 REMARK 500 ASP A 148 -12.41 78.14 REMARK 500 ARG A 158 -37.73 -132.19 REMARK 500 ALA A 159 75.86 60.86 REMARK 500 LYS A 161 156.30 -48.01 REMARK 500 ARG A 186 40.22 -109.35 REMARK 500 LYS A 194 4.95 -60.80 REMARK 500 MSE A 204 -82.89 -82.68 REMARK 500 ASP A 214 -36.45 -131.70 REMARK 500 ALA A 215 119.85 -161.89 REMARK 500 SER A 225 -43.48 -132.04 REMARK 500 ASN A 230 -14.19 69.80 REMARK 500 LEU A 235 -26.35 76.69 REMARK 500 ASN A 245 -80.22 44.91 REMARK 500 ALA A 246 45.59 -96.15 REMARK 500 LEU A 277 -2.60 86.27 REMARK 500 ARG A 288 73.35 -68.15 REMARK 500 TYR A 314 -35.88 -131.48 REMARK 500 SER A 316 -70.94 -83.81 REMARK 500 ALA A 323 61.88 -100.70 REMARK 500 LYS A 324 -150.20 -121.76 REMARK 500 LEU A 325 68.48 72.97 REMARK 500 ALA A 329 46.91 31.34 REMARK 500 VAL A 380 -76.58 -117.40 REMARK 500 ARG A 425 87.42 -159.98 REMARK 500 ALA A 435 -70.76 -62.88 REMARK 500 SER A 458 165.90 67.49 REMARK 500 ALA A 471 143.20 74.77 REMARK 500 GLN A 475 134.10 54.84 REMARK 500 LEU A 550 74.55 62.92 REMARK 500 ASN A 567 34.63 39.77 REMARK 500 GLU A 576 -137.84 40.45 REMARK 500 LEU A 594 143.10 65.65 REMARK 500 REMARK 500 THIS ENTRY HAS 56 RAMACHANDRAN OUTLIERS. 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 19 TYR A 20 144.04 REMARK 500 ILE A 233 SER A 234 -138.82 REMARK 500 ALA A 327 GLY A 328 144.29 REMARK 500 LYS A 616 GLN A 617 148.76 REMARK 500 THR A 678 GLN A 679 146.67 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7R8K A 1 789 UNP A0A2M8J4C7_9RHOB DBREF2 7R8K A A0A2M8J4C7 1 789 SEQADV 7R8K SER A -1 UNP A0A2M8J4C EXPRESSION TAG SEQADV 7R8K HIS A 0 UNP A0A2M8J4C EXPRESSION TAG SEQRES 1 A 791 SER HIS MSE THR LEU GLU THR THR LEU PHE PRO LEU GLU SEQRES 2 A 791 GLY LEU GLU GLY LEU THR ALA SER TYR GLN LEU TYR ALA SEQRES 3 A 791 VAL LYS GLY LEU SER GLY LEU ASP GLU THR GLU TYR HIS SEQRES 4 A 791 LYS ASN VAL ASN LEU LEU VAL ARG ARG LEU SER PHE SER SEQRES 5 A 791 MSE LYS ALA PRO PHE VAL ALA LEU SER ARG ASP GLY GLU SEQRES 6 A 791 GLN PHE ILE ALA VAL PRO ASN TYR VAL THR GLU PHE PRO SEQRES 7 A 791 VAL ASP HIS ARG VAL VAL ARG ALA MSE VAL LYS LEU VAL SEQRES 8 A 791 PRO THR GLY GLU PRO LEU ASN LEU ARG PHE ASP ALA ALA SEQRES 9 A 791 ASP ASP GLU TYR ASP GLY LEU ARG LEU ARG TYR LEU ASP SEQRES 10 A 791 PHE VAL LEU GLN GLN PRO LEU PHE ALA ASN HIS HIS LEU SEQRES 11 A 791 TRP GLN PRO GLY SER GLY GLN PRO PHE PHE HIS LYS LYS SEQRES 12 A 791 PRO LEU LYS ARG LEU ASP ASP VAL ASP LEU TYR ASP GLY SEQRES 13 A 791 VAL SER VAL ARG ALA ALA LYS HIS PRO GLU GLY GLY PHE SEQRES 14 A 791 GLY ILE VAL CYS ASP ALA ARG SER LYS PHE ILE THR HIS SEQRES 15 A 791 THR PRO ILE GLY ALA ARG ALA ASP ARG LYS ARG LEU GLY SEQRES 16 A 791 LYS LEU ILE ASN ARG SER CYS LEU TYR LYS MSE GLY ASP SEQRES 17 A 791 HIS TRP TYR GLN PHE ARG ILE ASP ALA VAL SER ASP TRP SEQRES 18 A 791 LYS VAL GLY GLU PRO SER LEU PHE GLU GLY ASN VAL PRO SEQRES 19 A 791 ILE SER LEU ALA GLN GLN LEU VAL ARG THR ALA GLY ASN SEQRES 20 A 791 ALA ALA PRO LYS SER ILE ILE ASP LEU ASP PRO GLU GLY SEQRES 21 A 791 GLY ALA LEU GLU TYR PHE THR SER THR ASN GLU ARG ARG SEQRES 22 A 791 MSE ALA PRO ALA GLU LEU CYS PHE LEU ILE GLU ASP THR SEQRES 23 A 791 HIS GLY ARG ARG ALA ALA LYS LEU GLN ARG GLN THR ILE SEQRES 24 A 791 LEU SER PRO SER GLU ARG ARG ALA ARG VAL ASN GLY PHE SEQRES 25 A 791 ILE ARG ARG TYR LEU SER GLU LEU ASN ILE GLY GLY ALA SEQRES 26 A 791 LYS LEU SER ALA GLY ALA ARG ALA HIS ALA PHE PHE THR SEQRES 27 A 791 GLU THR HIS MSE PRO PRO ALA LEU SER PHE GLY ASN GLY SEQRES 28 A 791 THR VAL LEU ALA PRO ASP THR SER LYS ASP ARG PHE GLN SEQRES 29 A 791 ALA MSE GLN GLU TYR SER SER MSE ARG ARG THR MSE MSE SEQRES 30 A 791 LEU ASP LYS LYS VAL GLY PHE PHE HIS GLN ASP VAL PHE SEQRES 31 A 791 PRO PRO GLN THR LEU LEU LEU PRO GLU SER VAL LYS LYS SEQRES 32 A 791 SER TRP GLY PRO ALA PHE ALA SER ASP PHE VAL GLY THR SEQRES 33 A 791 VAL GLN GLU LEU TYR PRO ALA GLY GLY TYR ARG PRO GLU SEQRES 34 A 791 ILE ILE GLU TYR ARG ASP LYS ALA TYR GLY GLY GLY VAL SEQRES 35 A 791 PRO GLY GLN MSE LYS ALA LEU LEU GLU VAL ALA GLU ARG SEQRES 36 A 791 GLY GLU ILE LYS SER GLY ASP VAL LEU VAL MSE LEU HIS SEQRES 37 A 791 ARG ILE ASN GLY ALA PRO ARG ALA GLN ASP LYS LEU ALA SEQRES 38 A 791 ALA MSE VAL CYS ASN GLU PHE GLU LYS ARG PHE GLY LYS SEQRES 39 A 791 ARG VAL GLN VAL ILE HIS SER ASP SER PRO GLY ARG GLY SEQRES 40 A 791 TYR LYS ARG ILE PHE LYS ASN ASP LYS PRO THR TYR VAL SEQRES 41 A 791 GLN GLN ARG GLY ARG GLY VAL ASN ILE LYS GLY TYR LEU SEQRES 42 A 791 LYS GLY ALA ALA LEU ASN LYS VAL CYS LEU GLY ASN SER SEQRES 43 A 791 ARG TRP PRO PHE VAL LEU ARG ASP PRO LEU ASN ALA ASP SEQRES 44 A 791 VAL THR ILE GLY ILE ASP VAL LYS ASN ASN MSE ALA VAL SEQRES 45 A 791 PHE THR MSE VAL ALA GLU GLY GLY ARG ILE VAL ARG VAL SEQRES 46 A 791 GLN ARG SER ARG SER ARG GLN ARG GLU GLN LEU LEU GLU SEQRES 47 A 791 SER GLN VAL THR GLN VAL ILE THR GLU MSE LEU SER LYS SEQRES 48 A 791 GLU LEU PRO GLU ILE LYS LYS GLN VAL GLN ARG VAL VAL SEQRES 49 A 791 ILE HIS ARG ASP GLY ARG ALA TRP PRO ALA GLU ILE ALA SEQRES 50 A 791 GLY ALA ARG LYS THR PHE ALA ASP MSE ALA GLU SER GLY SEQRES 51 A 791 LEU ILE ALA VAL ASP ALA ASP VAL SER VAL PHE GLU VAL SEQRES 52 A 791 LEU LYS SER SER PRO ALA PRO LEU ARG LEU PHE SER PHE SEQRES 53 A 791 GLU GLU PRO THR GLN GLU ASN PRO LYS GLY VAL ILE ASN SEQRES 54 A 791 PRO VAL LEU GLY SER TRP LEU LYS LEU SER GLU ASN ASP SEQRES 55 A 791 GLY TYR ILE CYS THR THR GLY ALA PRO LEU LEU LEU GLN SEQRES 56 A 791 GLY THR ALA ASP PRO LEU HIS VAL ARG LYS ALA PHE GLY SEQRES 57 A 791 PRO MSE ALA ILE GLU ASP ALA LEU LYS ASP VAL PHE ASP SEQRES 58 A 791 LEU SER CYS LEU THR TRP PRO LYS PRO ASP SER CYS MSE SEQRES 59 A 791 ARG LEU PRO LEU THR ILE LYS LEU CYS ASP ILE ALA LEU SEQRES 60 A 791 PHE ASP ASP ALA ALA GLU TYR ASP VAL ASP VAL VAL ARG SEQRES 61 A 791 PHE ALA ASP GLY ASN THR GLY GLU ALA SER ALA MODRES 7R8K MSE A 1 MET MODIFIED RESIDUE MODRES 7R8K MSE A 51 MET MODIFIED RESIDUE MODRES 7R8K MSE A 85 MET MODIFIED RESIDUE MODRES 7R8K MSE A 204 MET MODIFIED RESIDUE MODRES 7R8K MSE A 272 MET MODIFIED RESIDUE MODRES 7R8K MSE A 340 MET MODIFIED RESIDUE MODRES 7R8K MSE A 364 MET MODIFIED RESIDUE MODRES 7R8K MSE A 370 MET MODIFIED RESIDUE MODRES 7R8K MSE A 374 MET MODIFIED RESIDUE MODRES 7R8K MSE A 375 MET MODIFIED RESIDUE MODRES 7R8K MSE A 444 MET MODIFIED RESIDUE MODRES 7R8K MSE A 464 MET MODIFIED RESIDUE MODRES 7R8K MSE A 481 MET MODIFIED RESIDUE MODRES 7R8K MSE A 568 MET MODIFIED RESIDUE MODRES 7R8K MSE A 573 MET MODIFIED RESIDUE MODRES 7R8K MSE A 606 MET MODIFIED RESIDUE MODRES 7R8K MSE A 644 MET MODIFIED RESIDUE MODRES 7R8K MSE A 728 MET MODIFIED RESIDUE MODRES 7R8K MSE A 752 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 51 8 HET MSE A 85 8 HET MSE A 204 8 HET MSE A 272 8 HET MSE A 340 8 HET MSE A 364 8 HET MSE A 370 8 HET MSE A 374 8 HET MSE A 375 8 HET MSE A 444 8 HET MSE A 464 8 HET MSE A 481 8 HET MSE A 568 8 HET MSE A 573 8 HET MSE A 606 8 HET MSE A 644 8 HET MSE A 728 8 HET MSE A 752 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 19(C5 H11 N O2 SE) HELIX 1 AA1 GLU A 35 MSE A 51 1 17 HELIX 2 AA2 ASP A 104 ASP A 107 5 4 HELIX 3 AA3 GLY A 108 GLN A 119 1 12 HELIX 4 AA4 GLN A 119 ALA A 124 1 6 HELIX 5 AA5 ASP A 188 LYS A 194 1 7 HELIX 6 AA6 LEU A 235 THR A 242 1 8 HELIX 7 AA7 LYS A 249 ASP A 253 5 5 HELIX 8 AA8 SER A 299 LEU A 315 1 17 HELIX 9 AA9 PHE A 361 ASP A 377 1 17 HELIX 10 AB1 GLU A 397 LYS A 401 1 5 HELIX 11 AB2 TRP A 403 TYR A 419 1 17 HELIX 12 AB3 PRO A 420 GLY A 423 5 4 HELIX 13 AB4 GLY A 439 GLY A 454 1 16 HELIX 14 AB5 ASP A 476 PHE A 490 1 15 HELIX 15 AB6 SER A 501 ARG A 504 5 4 HELIX 16 AB7 ASN A 526 VAL A 539 1 14 HELIX 17 AB8 GLU A 596 LEU A 607 1 12 HELIX 18 AB9 TRP A 630 GLY A 648 1 19 HELIX 19 AC1 ALA A 729 SER A 741 1 13 HELIX 20 AC2 PRO A 755 ALA A 764 1 10 SHEET 1 AA1 2 THR A 2 GLU A 4 0 SHEET 2 AA1 2 ALA A 333 PHE A 335 -1 O PHE A 334 N LEU A 3 SHEET 1 AA2 5 LEU A 7 PRO A 9 0 SHEET 2 AA2 5 GLY A 168 THR A 179 -1 O ILE A 169 N PHE A 8 SHEET 3 AA2 5 VAL A 149 VAL A 157 -1 N ASP A 150 O ILE A 178 SHEET 4 AA2 5 PHE A 137 HIS A 139 -1 N PHE A 137 O VAL A 155 SHEET 5 AA2 5 LEU A 128 TRP A 129 -1 N TRP A 129 O PHE A 138 SHEET 1 AA3 3 TRP A 208 ARG A 212 0 SHEET 2 AA3 3 SER A 199 LYS A 203 -1 N TYR A 202 O TYR A 209 SHEET 3 AA3 3 CYS A 278 LEU A 280 -1 O PHE A 279 N LEU A 201 SHEET 1 AA4 2 LEU A 226 PHE A 227 0 SHEET 2 AA4 2 PRO A 232 ILE A 233 -1 O ILE A 233 N LEU A 226 SHEET 1 AA5 2 ALA A 260 PHE A 264 0 SHEET 2 AA5 2 ARG A 270 PRO A 274 -1 O ALA A 273 N LEU A 261 SHEET 1 AA6 2 LEU A 344 SER A 345 0 SHEET 2 AA6 2 VAL A 351 LEU A 352 -1 O LEU A 352 N LEU A 344 SHEET 1 AA7 4 GLU A 427 TYR A 431 0 SHEET 2 AA7 4 THR A 392 PRO A 396 1 N LEU A 393 O GLU A 427 SHEET 3 AA7 4 ASP A 460 LEU A 465 1 O MSE A 464 N LEU A 394 SHEET 4 AA7 4 ARG A 493 HIS A 498 1 O ILE A 497 N LEU A 465 SHEET 1 AA8 2 TYR A 506 LYS A 511 0 SHEET 2 AA8 2 LYS A 514 GLN A 519 -1 O LYS A 514 N LYS A 511 SHEET 1 AA9 3 VAL A 558 THR A 559 0 SHEET 2 AA9 3 MSE A 568 ALA A 575 -1 O VAL A 574 N THR A 559 SHEET 3 AA9 3 ILE A 580 ARG A 587 -1 O ILE A 580 N ALA A 575 SHEET 1 AB1 8 VAL A 558 THR A 559 0 SHEET 2 AB1 8 MSE A 568 ALA A 575 -1 O VAL A 574 N THR A 559 SHEET 3 AB1 8 GLY A 561 LYS A 565 -1 N ASP A 563 O VAL A 570 SHEET 4 AB1 8 ILE A 623 ASP A 626 1 O ASP A 626 N ILE A 562 SHEET 5 AB1 8 VAL A 658 LEU A 662 1 O VAL A 661 N ARG A 625 SHEET 6 AB1 8 LEU A 719 PHE A 725 -1 O HIS A 720 N LEU A 662 SHEET 7 AB1 8 ASP A 700 ILE A 703 -1 N ILE A 703 O LEU A 719 SHEET 8 AB1 8 TRP A 693 LYS A 695 -1 N LEU A 694 O TYR A 702 SHEET 1 AB2 2 SER A 673 PHE A 674 0 SHEET 2 AB2 2 VAL A 685 ILE A 686 -1 O ILE A 686 N SER A 673 LINK C HIS A 0 N MSE A 1 1555 1555 1.35 LINK C MSE A 1 N THR A 2 1555 1555 1.34 LINK C SER A 50 N MSE A 51 1555 1555 1.33 LINK C MSE A 51 N LYS A 52 1555 1555 1.34 LINK C ALA A 84 N MSE A 85 1555 1555 1.33 LINK C MSE A 85 N VAL A 86 1555 1555 1.33 LINK C LYS A 203 N MSE A 204 1555 1555 1.33 LINK C MSE A 204 N GLY A 205 1555 1555 1.31 LINK C ARG A 271 N MSE A 272 1555 1555 1.33 LINK C MSE A 272 N ALA A 273 1555 1555 1.34 LINK C HIS A 339 N MSE A 340 1555 1555 1.33 LINK C MSE A 340 N PRO A 341 1555 1555 1.33 LINK C ALA A 363 N MSE A 364 1555 1555 1.33 LINK C MSE A 364 N GLN A 365 1555 1555 1.33 LINK C SER A 369 N MSE A 370 1555 1555 1.33 LINK C MSE A 370 N ARG A 371 1555 1555 1.33 LINK C THR A 373 N MSE A 374 1555 1555 1.34 LINK C MSE A 374 N MSE A 375 1555 1555 1.32 LINK C MSE A 375 N LEU A 376 1555 1555 1.32 LINK C GLN A 443 N MSE A 444 1555 1555 1.32 LINK C MSE A 444 N LYS A 445 1555 1555 1.34 LINK C VAL A 463 N MSE A 464 1555 1555 1.32 LINK C MSE A 464 N LEU A 465 1555 1555 1.32 LINK C ALA A 480 N MSE A 481 1555 1555 1.32 LINK C MSE A 481 N VAL A 482 1555 1555 1.34 LINK C ASN A 567 N MSE A 568 1555 1555 1.32 LINK C MSE A 568 N ALA A 569 1555 1555 1.32 LINK C THR A 572 N MSE A 573 1555 1555 1.33 LINK C MSE A 573 N VAL A 574 1555 1555 1.32 LINK C GLU A 605 N MSE A 606 1555 1555 1.33 LINK C MSE A 606 N LEU A 607 1555 1555 1.32 LINK C ASP A 643 N MSE A 644 1555 1555 1.33 LINK C MSE A 644 N ALA A 645 1555 1555 1.34 LINK C PRO A 727 N MSE A 728 1555 1555 1.32 LINK C MSE A 728 N ALA A 729 1555 1555 1.33 LINK C CYS A 751 N MSE A 752 1555 1555 1.31 LINK C MSE A 752 N ARG A 753 1555 1555 1.33 CRYST1 199.813 199.813 199.813 90.00 90.00 90.00 I 2 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 0.005005 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005005 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005005 0.00000