HEADER ENDOCYTOSIS 14-FEB-18 5ZC4 TITLE CRYSTAL STRUCTURE OF RNF13 RING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF13; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: TRUNCATED RING DOMAIN; COMPND 5 SYNONYM: RING FINGER PROTEIN 13,RING-TYPE E3 UBIQUITIN TRANSFERASE COMPND 6 RNF13; COMPND 7 EC: 2.3.2.27; COMPND 8 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: RNF13, RZF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETSUMO2 KEYWDS UBIQUITIN RING E3 LIGASE, PA-TM-RING PROTEIN, RNF13, ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.B.DATTA,S.SARKAR REVDAT 2 27-MAR-24 5ZC4 1 REMARK REVDAT 1 27-FEB-19 5ZC4 0 JRNL AUTH S.SARKAR,A.B.DATTA JRNL TITL CRYSTAL STRUCTURE OF RNF13 RING DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.91 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 16599 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 795 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 22.6203 - 3.4591 0.98 2654 135 0.1419 0.1546 REMARK 3 2 3.4591 - 2.7471 1.00 2663 132 0.1827 0.2090 REMARK 3 3 2.7471 - 2.4003 1.00 2627 142 0.1837 0.2025 REMARK 3 4 2.4003 - 2.1810 1.00 2639 126 0.1823 0.2379 REMARK 3 5 2.1810 - 2.0248 1.00 2652 117 0.2012 0.2077 REMARK 3 6 2.0248 - 1.9055 0.99 2569 143 0.2388 0.2699 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.12 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 : 0.015 1242 REMARK 3 ANGLE : 1.431 1672 REMARK 3 CHIRALITY : 0.102 181 REMARK 3 PLANARITY : 0.012 213 REMARK 3 DIHEDRAL : 14.098 790 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 215:219 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.1659 36.7741 -9.9287 REMARK 3 T TENSOR REMARK 3 T11: 1.1434 T22: 1.4445 REMARK 3 T33: 0.6122 T12: 0.4490 REMARK 3 T13: 0.0767 T23: 0.0752 REMARK 3 L TENSOR REMARK 3 L11: 7.5112 L22: 6.6032 REMARK 3 L33: 1.3557 L12: 1.5250 REMARK 3 L13: -2.2746 L23: 1.5869 REMARK 3 S TENSOR REMARK 3 S11: -0.3167 S12: 0.4042 S13: 1.0110 REMARK 3 S21: -1.4603 S22: 0.0741 S23: -0.3024 REMARK 3 S31: -0.2398 S32: 1.2299 S33: -0.0160 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 220:230 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0776 24.8521 -6.6127 REMARK 3 T TENSOR REMARK 3 T11: 1.0409 T22: 0.8711 REMARK 3 T33: 0.8366 T12: 0.3459 REMARK 3 T13: 0.0402 T23: -0.2558 REMARK 3 L TENSOR REMARK 3 L11: 9.7398 L22: 2.8194 REMARK 3 L33: 8.3718 L12: 3.7399 REMARK 3 L13: -3.8602 L23: -4.4896 REMARK 3 S TENSOR REMARK 3 S11: -0.5128 S12: 1.6911 S13: -1.9076 REMARK 3 S21: -1.4531 S22: -0.3216 S23: -0.7702 REMARK 3 S31: 2.1120 S32: 0.6066 S33: 0.5784 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 231:235 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.1078 18.9910 8.1946 REMARK 3 T TENSOR REMARK 3 T11: 0.9767 T22: 0.4576 REMARK 3 T33: 1.3626 T12: -0.0680 REMARK 3 T13: 0.1117 T23: 0.0139 REMARK 3 L TENSOR REMARK 3 L11: 5.9260 L22: 4.0094 REMARK 3 L33: 4.9482 L12: -3.2924 REMARK 3 L13: 4.2063 L23: -0.2741 REMARK 3 S TENSOR REMARK 3 S11: -0.4755 S12: -0.7383 S13: -2.8403 REMARK 3 S21: 0.6241 S22: -0.3497 S23: 2.1469 REMARK 3 S31: 2.7372 S32: -0.9162 S33: 0.8596 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 236:255 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3815 28.0321 5.2272 REMARK 3 T TENSOR REMARK 3 T11: 0.4932 T22: 0.4553 REMARK 3 T33: 0.7238 T12: 0.0888 REMARK 3 T13: -0.1097 T23: -0.1201 REMARK 3 L TENSOR REMARK 3 L11: 7.6362 L22: 9.5925 REMARK 3 L33: 2.8387 L12: -0.3633 REMARK 3 L13: -1.7534 L23: 4.6083 REMARK 3 S TENSOR REMARK 3 S11: 0.2986 S12: 0.4427 S13: -2.0127 REMARK 3 S21: -0.3544 S22: -0.6663 S23: 1.3591 REMARK 3 S31: 0.7944 S32: -0.4206 S33: 0.3945 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 256:287 OR RESID 1001:1002 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.0787 33.2286 -0.0488 REMARK 3 T TENSOR REMARK 3 T11: 0.5405 T22: 0.5493 REMARK 3 T33: 0.3388 T12: 0.2996 REMARK 3 T13: 0.0267 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 6.3201 L22: 6.6276 REMARK 3 L33: 4.6275 L12: 0.4371 REMARK 3 L13: -1.4959 L23: 1.5568 REMARK 3 S TENSOR REMARK 3 S11: 0.6317 S12: 1.0726 S13: -0.2893 REMARK 3 S21: -1.1068 S22: -0.5397 S23: -0.2299 REMARK 3 S31: 0.2296 S32: 0.3769 S33: -0.0294 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN D AND RESID 216:219 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.9904 45.1954 16.1117 REMARK 3 T TENSOR REMARK 3 T11: 0.4026 T22: 0.9276 REMARK 3 T33: 1.0427 T12: -0.0764 REMARK 3 T13: 0.0286 T23: -0.0577 REMARK 3 L TENSOR REMARK 3 L11: 6.9491 L22: 2.0556 REMARK 3 L33: 9.1285 L12: 1.0403 REMARK 3 L13: -0.5478 L23: -3.4383 REMARK 3 S TENSOR REMARK 3 S11: 0.3201 S12: -0.0690 S13: 0.9974 REMARK 3 S21: -0.0572 S22: 0.7534 S23: -0.3624 REMARK 3 S31: -0.8338 S32: 0.0629 S33: -1.1657 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN D AND RESID 220:230 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.0294 33.6280 22.3279 REMARK 3 T TENSOR REMARK 3 T11: 0.3871 T22: 1.0790 REMARK 3 T33: 0.7932 T12: 0.1784 REMARK 3 T13: -0.0723 T23: -0.0564 REMARK 3 L TENSOR REMARK 3 L11: 4.6359 L22: 9.8933 REMARK 3 L33: 5.7555 L12: 6.1037 REMARK 3 L13: -1.5410 L23: -2.1014 REMARK 3 S TENSOR REMARK 3 S11: -0.6148 S12: -1.3556 S13: -0.4671 REMARK 3 S21: 0.3525 S22: 0.6306 S23: -1.2999 REMARK 3 S31: 0.0732 S32: 0.7397 S33: -0.0536 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN D AND RESID 231:235 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1072 21.4114 24.9880 REMARK 3 T TENSOR REMARK 3 T11: 0.9623 T22: 1.1507 REMARK 3 T33: 1.1201 T12: -0.0466 REMARK 3 T13: -0.0656 T23: 0.6009 REMARK 3 L TENSOR REMARK 3 L11: 0.2041 L22: 7.6351 REMARK 3 L33: 1.6908 L12: -1.0835 REMARK 3 L13: 0.1906 L23: -2.6997 REMARK 3 S TENSOR REMARK 3 S11: -0.0645 S12: -2.9781 S13: -2.8224 REMARK 3 S21: 2.0490 S22: 0.6235 S23: 1.3790 REMARK 3 S31: 1.6642 S32: -0.4079 S33: -0.5588 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN D AND RESID 236:255 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1524 28.2451 18.9469 REMARK 3 T TENSOR REMARK 3 T11: 0.5265 T22: 0.7967 REMARK 3 T33: 0.6320 T12: 0.1178 REMARK 3 T13: 0.0039 T23: 0.2744 REMARK 3 L TENSOR REMARK 3 L11: 2.6677 L22: 8.1242 REMARK 3 L33: 8.5092 L12: -2.2327 REMARK 3 L13: 3.9756 L23: -1.5358 REMARK 3 S TENSOR REMARK 3 S11: 0.3976 S12: -1.9835 S13: -1.7400 REMARK 3 S21: 0.5632 S22: 0.2009 S23: 0.3984 REMARK 3 S31: 1.5755 S32: -0.2724 S33: -0.5739 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN D AND ( RESID 256:287 OR RESID 1001:1002 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.7727 39.9927 19.3050 REMARK 3 T TENSOR REMARK 3 T11: 0.2784 T22: 0.8188 REMARK 3 T33: 0.5311 T12: 0.1025 REMARK 3 T13: -0.0235 T23: -0.1458 REMARK 3 L TENSOR REMARK 3 L11: 9.1620 L22: 7.5087 REMARK 3 L33: 7.0958 L12: 1.4877 REMARK 3 L13: 2.0662 L23: -2.1250 REMARK 3 S TENSOR REMARK 3 S11: -0.1346 S12: -1.6173 S13: 1.0928 REMARK 3 S21: 0.5721 S22: -0.0877 S23: -0.4244 REMARK 3 S31: -0.3090 S32: 0.7186 S33: 0.1942 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 5ZC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97947 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16628 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.906 REMARK 200 RESOLUTION RANGE LOW (A) : 45.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.81300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100% TACSIMATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 30.29667 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 15.14833 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.29667 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 15.14833 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 TOTAL BURIED SURFACE AREA: 20 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A1142 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 SER A 288 REMARK 465 GLN A 289 REMARK 465 GLY A 290 REMARK 465 MET D 215 REMARK 465 SER D 288 REMARK 465 GLN D 289 REMARK 465 GLY D 290 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 D 233 CG CD CE NZ 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 ASN A 216 33.36 72.48 REMARK 500 ASP A 238 -57.75 -125.64 REMARK 500 SER A 259 0.13 90.38 REMARK 500 GLU D 236 47.42 -89.36 REMARK 500 SER D 259 2.84 84.44 REMARK 500 THR D 274 -70.24 -118.67 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 240 SG REMARK 620 2 CYS A 243 SG 112.6 REMARK 620 3 HIS A 263 ND1 106.2 102.1 REMARK 620 4 CYS A 266 SG 120.1 105.6 108.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 258 SG REMARK 620 2 HIS A 260 ND1 109.1 REMARK 620 3 CYS A 278 SG 112.1 105.1 REMARK 620 4 CYS A 281 SG 102.4 114.7 113.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 240 SG REMARK 620 2 CYS D 243 SG 114.6 REMARK 620 3 HIS D 263 ND1 106.3 101.8 REMARK 620 4 CYS D 266 SG 115.2 109.9 107.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 258 SG REMARK 620 2 HIS D 260 ND1 106.1 REMARK 620 3 CYS D 278 SG 104.9 108.3 REMARK 620 4 CYS D 281 SG 114.5 107.8 114.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 1002 DBREF 5ZC4 A 216 290 UNP O43567 RNF13_HUMAN 216 290 DBREF 5ZC4 D 216 290 UNP O43567 RNF13_HUMAN 216 290 SEQADV 5ZC4 MET A 215 UNP O43567 EXPRESSION TAG SEQADV 5ZC4 MET D 215 UNP O43567 EXPRESSION TAG SEQRES 1 A 76 MET ASN ARG LEU ARG LYS ASP GLN LEU LYS LYS LEU PRO SEQRES 2 A 76 VAL HIS LYS PHE LYS LYS GLY ASP GLU TYR ASP VAL CYS SEQRES 3 A 76 ALA ILE CYS LEU ASP GLU TYR GLU ASP GLY ASP LYS LEU SEQRES 4 A 76 ARG ILE LEU PRO CYS SER HIS ALA TYR HIS CYS LYS CYS SEQRES 5 A 76 VAL ASP PRO TRP LEU THR LYS THR LYS LYS THR CYS PRO SEQRES 6 A 76 VAL CYS LYS GLN LYS VAL VAL PRO SER GLN GLY SEQRES 1 D 76 MET ASN ARG LEU ARG LYS ASP GLN LEU LYS LYS LEU PRO SEQRES 2 D 76 VAL HIS LYS PHE LYS LYS GLY ASP GLU TYR ASP VAL CYS SEQRES 3 D 76 ALA ILE CYS LEU ASP GLU TYR GLU ASP GLY ASP LYS LEU SEQRES 4 D 76 ARG ILE LEU PRO CYS SER HIS ALA TYR HIS CYS LYS CYS SEQRES 5 D 76 VAL ASP PRO TRP LEU THR LYS THR LYS LYS THR CYS PRO SEQRES 6 D 76 VAL CYS LYS GLN LYS VAL VAL PRO SER GLN GLY HET ZN A1001 1 HET ZN A1002 1 HET ZN D1001 1 HET ZN D1002 1 HETNAM ZN ZINC ION FORMUL 3 ZN 4(ZN 2+) FORMUL 7 HOH *78(H2 O) HELIX 1 AA1 ARG A 219 LYS A 224 1 6 HELIX 2 AA2 CYS A 264 THR A 274 1 11 HELIX 3 AA3 ARG D 219 LYS D 224 1 6 HELIX 4 AA4 CYS D 264 THR D 274 1 11 SHEET 1 AA1 3 VAL A 228 LYS A 230 0 SHEET 2 AA1 3 LYS A 252 ILE A 255 -1 O LEU A 253 N HIS A 229 SHEET 3 AA1 3 ALA A 261 HIS A 263 -1 O TYR A 262 N ARG A 254 SHEET 1 AA2 3 VAL D 228 LYS D 230 0 SHEET 2 AA2 3 LYS D 252 ILE D 255 -1 O LEU D 253 N HIS D 229 SHEET 3 AA2 3 ALA D 261 HIS D 263 -1 O TYR D 262 N ARG D 254 LINK SG CYS A 240 ZN ZN A1001 1555 1555 2.31 LINK SG CYS A 243 ZN ZN A1001 1555 1555 2.28 LINK SG CYS A 258 ZN ZN A1002 1555 1555 2.35 LINK ND1 HIS A 260 ZN ZN A1002 1555 1555 2.13 LINK ND1 HIS A 263 ZN ZN A1001 1555 1555 2.07 LINK SG CYS A 266 ZN ZN A1001 1555 1555 2.36 LINK SG CYS A 278 ZN ZN A1002 1555 1555 2.23 LINK SG CYS A 281 ZN ZN A1002 1555 1555 2.25 LINK SG CYS D 240 ZN ZN D1001 1555 1555 2.35 LINK SG CYS D 243 ZN ZN D1001 1555 1555 2.35 LINK SG CYS D 258 ZN ZN D1002 1555 1555 2.39 LINK ND1 HIS D 260 ZN ZN D1002 1555 1555 2.09 LINK ND1 HIS D 263 ZN ZN D1001 1555 1555 2.10 LINK SG CYS D 266 ZN ZN D1001 1555 1555 2.34 LINK SG CYS D 278 ZN ZN D1002 1555 1555 2.29 LINK SG CYS D 281 ZN ZN D1002 1555 1555 2.23 SITE 1 AC1 4 CYS A 240 CYS A 243 HIS A 263 CYS A 266 SITE 1 AC2 4 CYS A 258 HIS A 260 CYS A 278 CYS A 281 SITE 1 AC3 4 CYS D 240 CYS D 243 HIS D 263 CYS D 266 SITE 1 AC4 4 CYS D 258 HIS D 260 CYS D 278 CYS D 281 CRYST1 90.338 90.338 45.445 90.00 90.00 120.00 P 62 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 0.011070 0.006391 0.000000 0.00000 SCALE2 0.000000 0.012782 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022005 0.00000