HEADER DNA BINDING PROTEIN 28-MAR-24 8YVB TITLE CRYSTAL STRUCTURE OF CAENORHABDITIS ELEGANS ZIM-1 ZF1-2-CTD DOMAIN IN TITLE 2 COMPLEX WITH CHROMOSOME II/III PAIRING CENTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: C2H2-TYPE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*TP*GP*GP*TP*CP*TP*GP*CP*TP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*AP*GP*CP*AP*GP*AP*CP*CP*AP*A)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: ZIM-1, CELE_T07G12.6, T07G12.6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 10 ORGANISM_TAXID: 6239; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 14 ORGANISM_TAXID: 6239 KEYWDS DOUBLE STRANDED DNA BINDING PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.D.LI,M.L.LI REVDAT 1 11-DEC-24 8YVB 0 JRNL AUTH M.LI,C.ZHU,Z.XU,M.XU,Y.KUANG,X.HOU,X.HUANG,M.LV,Y.LIU, JRNL AUTH 2 Y.ZHANG,Z.XU,X.HAN,S.WANG,Y.SHI,S.GUANG,F.LI JRNL TITL STRUCTURAL BASIS FOR C. ELEGANS PAIRING CENTER DNA BINDING JRNL TITL 2 SPECIFICITY BY THE ZIM/HIM-8 FAMILY PROTEINS. JRNL REF NAT COMMUN V. 15 10355 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39609407 JRNL DOI 10.1038/S41467-024-54548-9 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 14122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 692 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 19.7000 - 3.2500 1.00 2817 152 0.1684 0.2208 REMARK 3 2 3.2400 - 2.5800 1.00 2739 126 0.1980 0.2257 REMARK 3 3 2.5800 - 2.2500 1.00 2705 141 0.1988 0.2586 REMARK 3 4 2.2500 - 2.0500 1.00 2677 142 0.2069 0.2783 REMARK 3 5 2.0500 - 1.9000 0.95 2492 131 0.2246 0.2615 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.003 1365 REMARK 3 ANGLE : 0.585 1917 REMARK 3 CHIRALITY : 0.040 204 REMARK 3 PLANARITY : 0.003 167 REMARK 3 DIHEDRAL : 26.111 538 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 454 THROUGH 493 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5443 -19.3807 9.4904 REMARK 3 T TENSOR REMARK 3 T11: 0.1750 T22: 0.1679 REMARK 3 T33: 0.1159 T12: -0.0427 REMARK 3 T13: 0.0850 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.4199 L22: 0.6916 REMARK 3 L33: 0.8203 L12: -0.2372 REMARK 3 L13: -0.1888 L23: 0.0094 REMARK 3 S TENSOR REMARK 3 S11: 0.0621 S12: 0.4871 S13: -0.0364 REMARK 3 S21: -0.5493 S22: -0.0711 S23: -0.2203 REMARK 3 S31: -0.1834 S32: 0.0426 S33: 0.0175 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 494 THROUGH 516 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5877 -36.6908 15.3719 REMARK 3 T TENSOR REMARK 3 T11: 0.0983 T22: 0.1632 REMARK 3 T33: 0.1869 T12: -0.0062 REMARK 3 T13: 0.0084 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 2.4202 L22: 2.3141 REMARK 3 L33: 1.9269 L12: 0.5326 REMARK 3 L13: -0.2099 L23: -0.5687 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: -0.1489 S13: -0.5209 REMARK 3 S21: -0.2520 S22: -0.2203 S23: -0.3149 REMARK 3 S31: 0.2096 S32: 0.2824 S33: 0.1155 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 517 THROUGH 536 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8367 -31.7739 23.8883 REMARK 3 T TENSOR REMARK 3 T11: 0.2205 T22: 0.1810 REMARK 3 T33: 0.2478 T12: -0.0539 REMARK 3 T13: 0.0574 T23: 0.0733 REMARK 3 L TENSOR REMARK 3 L11: 0.2545 L22: 1.0788 REMARK 3 L33: 0.6604 L12: 0.4407 REMARK 3 L13: 0.3974 L23: 0.5541 REMARK 3 S TENSOR REMARK 3 S11: -0.0797 S12: -0.3176 S13: -0.1914 REMARK 3 S21: 0.2340 S22: -0.1494 S23: 0.1929 REMARK 3 S31: 0.3728 S32: -0.1519 S33: -0.1110 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 537 THROUGH 558 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.1314 -16.8551 16.7125 REMARK 3 T TENSOR REMARK 3 T11: 0.1647 T22: 0.1853 REMARK 3 T33: 0.2217 T12: -0.0759 REMARK 3 T13: 0.0563 T23: -0.0384 REMARK 3 L TENSOR REMARK 3 L11: 1.0233 L22: 2.7293 REMARK 3 L33: 1.7628 L12: -0.4165 REMARK 3 L13: -0.9709 L23: 0.3611 REMARK 3 S TENSOR REMARK 3 S11: -0.2141 S12: 0.0059 S13: -0.0823 REMARK 3 S21: 0.0730 S22: 0.2440 S23: -0.5462 REMARK 3 S31: -0.1386 S32: 0.5392 S33: 0.1773 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.4339 -18.9784 13.1304 REMARK 3 T TENSOR REMARK 3 T11: 0.1433 T22: 0.1596 REMARK 3 T33: 0.1415 T12: 0.0227 REMARK 3 T13: -0.0207 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.6279 L22: 1.5545 REMARK 3 L33: 1.3280 L12: -0.1742 REMARK 3 L13: 0.2441 L23: -0.1582 REMARK 3 S TENSOR REMARK 3 S11: 0.0149 S12: 0.1168 S13: -0.0271 REMARK 3 S21: -0.2719 S22: 0.0351 S23: 0.0782 REMARK 3 S31: -0.0850 S32: -0.1866 S33: -0.0887 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3212 -21.1506 11.9505 REMARK 3 T TENSOR REMARK 3 T11: 0.2068 T22: 0.1651 REMARK 3 T33: 0.1162 T12: 0.0054 REMARK 3 T13: -0.0441 T23: -0.0276 REMARK 3 L TENSOR REMARK 3 L11: 0.4876 L22: 0.0452 REMARK 3 L33: 1.6999 L12: -0.0413 REMARK 3 L13: 0.4581 L23: 0.0953 REMARK 3 S TENSOR REMARK 3 S11: 0.0954 S12: 0.1202 S13: -0.0553 REMARK 3 S21: -0.4114 S22: -0.0856 S23: 0.0462 REMARK 3 S31: -0.0707 S32: -0.3289 S33: 0.0538 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 8YVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300046443. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-20 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14363 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.90 REMARK 200 R MERGE FOR SHELL (I) : 0.97200 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: 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 (%): 40.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG 600 AND 0.1 M HEPES, PH REMARK 280 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.78200 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 50.78200 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 1.000000 0.000000 0.000000 27.88350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.23200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.88350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.23200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.78200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.88350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.23200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.78200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.88350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.23200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 118 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 120 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 433 REMARK 465 PRO A 434 REMARK 465 HIS A 435 REMARK 465 MET A 436 REMARK 465 SER A 437 REMARK 465 PHE A 438 REMARK 465 ALA A 439 REMARK 465 VAL A 440 REMARK 465 PRO A 441 REMARK 465 LEU A 442 REMARK 465 VAL A 443 REMARK 465 GLN A 444 REMARK 465 SER A 445 REMARK 465 ARG A 446 REMARK 465 SER A 447 REMARK 465 LYS A 448 REMARK 465 GLN A 449 REMARK 465 LYS A 450 REMARK 465 ASP A 451 REMARK 465 GLU A 452 REMARK 465 MET A 453 REMARK 465 GLY A 559 REMARK 465 THR A 560 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 536 CG CD CE NZ REMARK 470 ARG A 552 CG CD NE CZ NH1 NH2 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 C 110 O HOH C 110 3555 2.09 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 DA C 5 O4' - C1' - N9 ANGL. DEV. = 2.4 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 LYS A 536 31.21 -97.44 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 A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 461 SG REMARK 620 2 CYS A 466 SG 115.4 REMARK 620 3 HIS A 484 NE2 104.1 105.4 REMARK 620 4 HIS A 488 NE2 112.1 109.7 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 496 SG REMARK 620 2 CYS A 499 SG 121.3 REMARK 620 3 HIS A 512 NE2 106.3 104.5 REMARK 620 4 HIS A 517 NE2 101.6 116.4 105.6 REMARK 620 N 1 2 3 DBREF 8YVB A 437 560 UNP B2MZC6 B2MZC6_CAEEL 437 560 DBREF 8YVB B 1 11 PDB 8YVB 8YVB 1 11 DBREF 8YVB C 2 11 PDB 8YVB 8YVB 2 11 SEQADV 8YVB GLY A 433 UNP B2MZC6 EXPRESSION TAG SEQADV 8YVB PRO A 434 UNP B2MZC6 EXPRESSION TAG SEQADV 8YVB HIS A 435 UNP B2MZC6 EXPRESSION TAG SEQADV 8YVB MET A 436 UNP B2MZC6 EXPRESSION TAG SEQRES 1 A 128 GLY PRO HIS MET SER PHE ALA VAL PRO LEU VAL GLN SER SEQRES 2 A 128 ARG SER LYS GLN LYS ASP GLU MET ASN LYS VAL HIS ILE SEQRES 3 A 128 ILE LYS CYS HIS PHE ASP LYS CYS ASN LYS SER TYR ASN SEQRES 4 A 128 TRP ARG LYS LYS TYR GLY LYS LEU ARG LEU VAL ASP HIS SEQRES 5 A 128 ALA PHE THR HIS VAL PRO HIS LEU LYS MET LYS CYS ASN SEQRES 6 A 128 PHE CYS ASP TYR MET CYS LYS GLY ILE ARG ASN ILE ARG SEQRES 7 A 128 LEU HIS HIS LYS LYS SER HIS PRO ASP GLU GLN LEU THR SEQRES 8 A 128 GLY PHE GLY ILE LYS SER VAL VAL ARG THR SER LYS LYS SEQRES 9 A 128 GLY LYS ASP LEU ALA LYS VAL TRP ASP GLU CYS PHE LYS SEQRES 10 A 128 LYS ASN ARG VAL LEU GLN HIS GLY SER GLY THR SEQRES 1 B 11 DT DT DG DG DT DC DT DG DC DT DA SEQRES 1 C 10 DA DG DC DA DG DA DC DC DA DA HET ZN A 601 1 HET ZN A 602 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *110(H2 O) HELIX 1 AA1 ARG A 473 GLY A 477 5 5 HELIX 2 AA2 LYS A 478 THR A 487 1 10 HELIX 3 AA3 GLY A 505 HIS A 517 1 13 HELIX 4 AA4 GLY A 526 LYS A 528 5 3 HELIX 5 AA5 SER A 529 SER A 534 1 6 HELIX 6 AA6 LYS A 536 LYS A 549 1 14 HELIX 7 AA7 ASN A 551 GLN A 555 5 5 SHEET 1 AA1 2 HIS A 457 LYS A 460 0 SHEET 2 AA1 2 SER A 469 TRP A 472 -1 O TRP A 472 N HIS A 457 SHEET 1 AA2 2 MET A 494 LYS A 495 0 SHEET 2 AA2 2 MET A 502 CYS A 503 -1 O CYS A 503 N MET A 494 LINK SG CYS A 461 ZN ZN A 601 1555 1555 2.27 LINK SG CYS A 466 ZN ZN A 601 1555 1555 2.34 LINK NE2 HIS A 484 ZN ZN A 601 1555 1555 2.18 LINK NE2 HIS A 488 ZN ZN A 601 1555 1555 2.00 LINK SG CYS A 496 ZN ZN A 602 1555 1555 2.23 LINK SG CYS A 499 ZN ZN A 602 1555 1555 2.29 LINK NE2 HIS A 512 ZN ZN A 602 1555 1555 2.09 LINK NE2 HIS A 517 ZN ZN A 602 1555 1555 2.07 CRYST1 55.767 62.464 101.564 90.00 90.00 90.00 C 2 2 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 0.017932 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009846 0.00000 CONECT 65 1296 CONECT 109 1296 CONECT 272 1296 CONECT 305 1296 CONECT 369 1297 CONECT 394 1297 CONECT 505 1297 CONECT 549 1297 CONECT 1296 65 109 272 305 CONECT 1297 369 394 505 549 MASTER 427 0 2 7 4 0 0 6 1404 3 10 12 END