HEADER HYDROLASE 02-JUN-11 3SAF TITLE CRYSTAL STRUCTURE OF THE HUMAN RRP6 CATALYTIC DOMAIN WITH D313N TITLE 2 MUTATION IN THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXOSOME COMPONENT 10; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 180-606; COMPND 5 SYNONYM: RRP6, AUTOANTIGEN PM/SCL 2, P100 POLYMYOSITIS-SCLERODERMA COMPND 6 OVERLAP SYNDROME-ASSOCIATED AUTOANTIGEN, POLYMYOSITIS/SCLERODERMA COMPND 7 AUTOANTIGEN 100 KDA, PM/SCL-100, POLYMYOSITIS/SCLERODERMA AUTOANTIGEN COMPND 8 2; COMPND 9 EC: 3.1.13.-; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: EXOSC10, PMSCL, PMSCL2, RRP6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CP RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSMT3 SUMO FUSION KEYWDS EXORIBONUCLEASE, RNA EXOSOME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.JANUSZYK,Q.LIU,C.D.LIMA REVDAT 4 13-SEP-23 3SAF 1 REMARK SEQADV LINK REVDAT 3 03-AUG-11 3SAF 1 JRNL REVDAT 2 13-JUL-11 3SAF 1 JRNL REVDAT 1 06-JUL-11 3SAF 0 JRNL AUTH K.JANUSZYK,Q.LIU,C.D.LIMA JRNL TITL ACTIVITIES OF HUMAN RRP6 AND STRUCTURE OF THE HUMAN RRP6 JRNL TITL 2 CATALYTIC DOMAIN. JRNL REF RNA V. 17 1566 2011 JRNL REFN ISSN 1355-8382 JRNL PMID 21705430 JRNL DOI 10.1261/RNA.2763111 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1418335.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 74970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3730 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 11991 REMARK 3 BIN R VALUE (WORKING SET) : 0.3370 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 590 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6305 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.83000 REMARK 3 B22 (A**2) : -8.83000 REMARK 3 B33 (A**2) : 17.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.48 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.490 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.050 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.230 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 41.18 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION-CDL2.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION-CDL2.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3SAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000065963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : KOHZU HLD8-24 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75251 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.42100 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2HBJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG6000, 1.5 M SODIUM CHLORIDE, 0.4 REMARK 280 MM YTTRIUM(III) TRICHLORIDE, PH 8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 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 -Y,X,Z REMARK 290 4555 Y,-X,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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 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: MONOMERIC 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 222 REMARK 465 ARG A 223 REMARK 465 PRO A 224 REMARK 465 GLN A 225 REMARK 465 ASP A 226 REMARK 465 ARG A 227 REMARK 465 PRO A 228 REMARK 465 GLU A 229 REMARK 465 ASP A 230 REMARK 465 LEU A 231 REMARK 465 ASP A 232 REMARK 465 VAL A 233 REMARK 465 PRO A 234 REMARK 465 PRO A 235 REMARK 465 ALA A 236 REMARK 465 LEU A 237 REMARK 465 ALA A 238 REMARK 465 ASP A 239 REMARK 465 PHE A 240 REMARK 465 ILE A 241 REMARK 465 HIS A 242 REMARK 465 GLN A 243 REMARK 465 GLN A 244 REMARK 465 ARG A 245 REMARK 465 THR A 246 REMARK 465 GLN A 247 REMARK 465 GLN A 248 REMARK 465 VAL A 249 REMARK 465 GLU A 250 REMARK 465 GLY A 589 REMARK 465 VAL A 590 REMARK 465 LYS A 591 REMARK 465 LYS A 592 REMARK 465 SER A 593 REMARK 465 GLY A 594 REMARK 465 PRO A 595 REMARK 465 LEU A 596 REMARK 465 PRO A 597 REMARK 465 SER A 598 REMARK 465 ALA A 599 REMARK 465 GLU A 600 REMARK 465 ARG A 601 REMARK 465 LEU A 602 REMARK 465 GLU A 603 REMARK 465 ASN A 604 REMARK 465 VAL A 605 REMARK 465 LEU A 606 REMARK 465 ARG B 221 REMARK 465 GLU B 222 REMARK 465 ARG B 223 REMARK 465 PRO B 224 REMARK 465 GLN B 225 REMARK 465 ASP B 226 REMARK 465 ARG B 227 REMARK 465 PRO B 228 REMARK 465 GLU B 229 REMARK 465 ASP B 230 REMARK 465 LEU B 231 REMARK 465 ASP B 232 REMARK 465 VAL B 233 REMARK 465 PRO B 234 REMARK 465 PRO B 235 REMARK 465 ALA B 236 REMARK 465 LEU B 237 REMARK 465 ALA B 238 REMARK 465 ASP B 239 REMARK 465 PHE B 240 REMARK 465 ILE B 241 REMARK 465 HIS B 242 REMARK 465 GLN B 243 REMARK 465 GLN B 244 REMARK 465 ARG B 245 REMARK 465 THR B 246 REMARK 465 GLN B 247 REMARK 465 GLN B 248 REMARK 465 VAL B 249 REMARK 465 GLU B 250 REMARK 465 GLY B 589 REMARK 465 VAL B 590 REMARK 465 LYS B 591 REMARK 465 LYS B 592 REMARK 465 SER B 593 REMARK 465 GLY B 594 REMARK 465 PRO B 595 REMARK 465 LEU B 596 REMARK 465 PRO B 597 REMARK 465 SER B 598 REMARK 465 ALA B 599 REMARK 465 GLU B 600 REMARK 465 ARG B 601 REMARK 465 LEU B 602 REMARK 465 GLU B 603 REMARK 465 ASN B 604 REMARK 465 VAL B 605 REMARK 465 LEU B 606 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 B 220 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS B 499 CG CD CE NZ REMARK 470 LYS B 500 CG CD CE NZ REMARK 470 HIS B 501 CG ND1 CD2 CE1 NE2 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 OE2 GLU A 489 Y YT3 A 1 1.73 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 PRO A 211 152.79 -47.17 REMARK 500 ASP A 252 -132.63 -102.34 REMARK 500 MET A 253 -37.16 178.86 REMARK 500 SER A 292 14.05 -147.32 REMARK 500 ARG A 320 60.37 -107.87 REMARK 500 SER A 321 138.27 -172.99 REMARK 500 ASN A 385 80.56 80.69 REMARK 500 ASN A 460 -1.20 63.71 REMARK 500 TYR A 491 12.07 -63.10 REMARK 500 LYS A 497 55.63 -106.46 REMARK 500 GLN A 498 -40.19 -179.70 REMARK 500 LYS A 499 100.13 177.76 REMARK 500 LEU A 532 98.65 -165.90 REMARK 500 SER A 584 1.45 -65.37 REMARK 500 LYS B 186 7.94 -173.92 REMARK 500 SER B 217 175.82 -56.08 REMARK 500 PRO B 277 145.54 -37.66 REMARK 500 ASN B 385 91.21 81.17 REMARK 500 ASP B 414 62.48 -114.60 REMARK 500 SER B 415 144.60 -36.11 REMARK 500 LEU B 421 45.53 -106.12 REMARK 500 ILE B 485 91.62 -163.46 REMARK 500 LYS B 499 6.86 55.29 REMARK 500 ASP B 525 60.00 61.97 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 YT3 A 1 Y REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 488 OD2 REMARK 620 2 ASP A 488 OD1 45.5 REMARK 620 3 GLU A 489 OE1 90.0 80.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 31 O REMARK 620 2 HOH A 38 O 158.8 REMARK 620 3 HOH A 74 O 84.3 92.0 REMARK 620 4 ASN A 313 OD1 90.4 68.4 79.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 165 O REMARK 620 2 ASN B 313 OD1 72.5 REMARK 620 3 HOH B 647 O 105.8 102.2 REMARK 620 4 HOH B 648 O 91.1 67.6 157.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YT3 B 2 Y REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 488 OD1 REMARK 620 2 ASP B 488 OD2 41.9 REMARK 620 3 GLU B 489 OE2 95.1 75.8 REMARK 620 4 GLU B 489 OE1 80.9 101.7 58.4 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 MG A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SAG RELATED DB: PDB REMARK 900 RELATED ID: 3SAH RELATED DB: PDB DBREF 3SAF A 180 606 UNP Q01780 EXOSX_HUMAN 180 606 DBREF 3SAF B 180 606 UNP Q01780 EXOSX_HUMAN 180 606 SEQADV 3SAF SER A 179 UNP Q01780 EXPRESSION TAG SEQADV 3SAF ASN A 313 UNP Q01780 ASP 313 ENGINEERED MUTATION SEQADV 3SAF SER B 179 UNP Q01780 EXPRESSION TAG SEQADV 3SAF ASN B 313 UNP Q01780 ASP 313 ENGINEERED MUTATION SEQRES 1 A 428 SER ILE ILE ARG PRO GLN LEU LYS PHE ARG GLU LYS ILE SEQRES 2 A 428 ASP ASN SER ASN THR PRO PHE LEU PRO LYS ILE PHE ILE SEQRES 3 A 428 LYS PRO ASN ALA GLN LYS PRO LEU PRO GLN ALA LEU SER SEQRES 4 A 428 LYS GLU ARG ARG GLU ARG PRO GLN ASP ARG PRO GLU ASP SEQRES 5 A 428 LEU ASP VAL PRO PRO ALA LEU ALA ASP PHE ILE HIS GLN SEQRES 6 A 428 GLN ARG THR GLN GLN VAL GLU GLN ASP MET PHE ALA HIS SEQRES 7 A 428 PRO TYR GLN TYR GLU LEU ASN HIS PHE THR PRO ALA ASP SEQRES 8 A 428 ALA VAL LEU GLN LYS PRO GLN PRO GLN LEU TYR ARG PRO SEQRES 9 A 428 ILE GLU GLU THR PRO CYS HIS PHE ILE SER SER LEU ASP SEQRES 10 A 428 GLU LEU VAL GLU LEU ASN GLU LYS LEU LEU ASN CYS GLN SEQRES 11 A 428 GLU PHE ALA VAL ASN LEU GLU HIS HIS SER TYR ARG SER SEQRES 12 A 428 PHE LEU GLY LEU THR CYS LEU MET GLN ILE SER THR ARG SEQRES 13 A 428 THR GLU ASP PHE ILE ILE ASP THR LEU GLU LEU ARG SER SEQRES 14 A 428 ASP MET TYR ILE LEU ASN GLU SER LEU THR ASP PRO ALA SEQRES 15 A 428 ILE VAL LYS VAL PHE HIS GLY ALA ASP SER ASP ILE GLU SEQRES 16 A 428 TRP LEU GLN LYS ASP PHE GLY LEU TYR VAL VAL ASN MET SEQRES 17 A 428 PHE ASP THR HIS GLN ALA ALA ARG LEU LEU ASN LEU GLY SEQRES 18 A 428 ARG HIS SER LEU ASP HIS LEU LEU LYS LEU TYR CYS ASN SEQRES 19 A 428 VAL ASP SER ASN LYS GLN TYR GLN LEU ALA ASP TRP ARG SEQRES 20 A 428 ILE ARG PRO LEU PRO GLU GLU MET LEU SER TYR ALA ARG SEQRES 21 A 428 ASP ASP THR HIS TYR LEU LEU TYR ILE TYR ASP LYS MET SEQRES 22 A 428 ARG LEU GLU MET TRP GLU ARG GLY ASN GLY GLN PRO VAL SEQRES 23 A 428 GLN LEU GLN VAL VAL TRP GLN ARG SER ARG ASP ILE CYS SEQRES 24 A 428 LEU LYS LYS PHE ILE LYS PRO ILE PHE THR ASP GLU SER SEQRES 25 A 428 TYR LEU GLU LEU TYR ARG LYS GLN LYS LYS HIS LEU ASN SEQRES 26 A 428 THR GLN GLN LEU THR ALA PHE GLN LEU LEU PHE ALA TRP SEQRES 27 A 428 ARG ASP LYS THR ALA ARG ARG GLU ASP GLU SER TYR GLY SEQRES 28 A 428 TYR VAL LEU PRO ASN HIS MET MET LEU LYS ILE ALA GLU SEQRES 29 A 428 GLU LEU PRO LYS GLU PRO GLN GLY ILE ILE ALA CYS CYS SEQRES 30 A 428 ASN PRO VAL PRO PRO LEU VAL ARG GLN GLN ILE ASN GLU SEQRES 31 A 428 MET HIS LEU LEU ILE GLN GLN ALA ARG GLU MET PRO LEU SEQRES 32 A 428 LEU LYS SER GLU VAL ALA ALA GLY VAL LYS LYS SER GLY SEQRES 33 A 428 PRO LEU PRO SER ALA GLU ARG LEU GLU ASN VAL LEU SEQRES 1 B 428 SER ILE ILE ARG PRO GLN LEU LYS PHE ARG GLU LYS ILE SEQRES 2 B 428 ASP ASN SER ASN THR PRO PHE LEU PRO LYS ILE PHE ILE SEQRES 3 B 428 LYS PRO ASN ALA GLN LYS PRO LEU PRO GLN ALA LEU SER SEQRES 4 B 428 LYS GLU ARG ARG GLU ARG PRO GLN ASP ARG PRO GLU ASP SEQRES 5 B 428 LEU ASP VAL PRO PRO ALA LEU ALA ASP PHE ILE HIS GLN SEQRES 6 B 428 GLN ARG THR GLN GLN VAL GLU GLN ASP MET PHE ALA HIS SEQRES 7 B 428 PRO TYR GLN TYR GLU LEU ASN HIS PHE THR PRO ALA ASP SEQRES 8 B 428 ALA VAL LEU GLN LYS PRO GLN PRO GLN LEU TYR ARG PRO SEQRES 9 B 428 ILE GLU GLU THR PRO CYS HIS PHE ILE SER SER LEU ASP SEQRES 10 B 428 GLU LEU VAL GLU LEU ASN GLU LYS LEU LEU ASN CYS GLN SEQRES 11 B 428 GLU PHE ALA VAL ASN LEU GLU HIS HIS SER TYR ARG SER SEQRES 12 B 428 PHE LEU GLY LEU THR CYS LEU MET GLN ILE SER THR ARG SEQRES 13 B 428 THR GLU ASP PHE ILE ILE ASP THR LEU GLU LEU ARG SER SEQRES 14 B 428 ASP MET TYR ILE LEU ASN GLU SER LEU THR ASP PRO ALA SEQRES 15 B 428 ILE VAL LYS VAL PHE HIS GLY ALA ASP SER ASP ILE GLU SEQRES 16 B 428 TRP LEU GLN LYS ASP PHE GLY LEU TYR VAL VAL ASN MET SEQRES 17 B 428 PHE ASP THR HIS GLN ALA ALA ARG LEU LEU ASN LEU GLY SEQRES 18 B 428 ARG HIS SER LEU ASP HIS LEU LEU LYS LEU TYR CYS ASN SEQRES 19 B 428 VAL ASP SER ASN LYS GLN TYR GLN LEU ALA ASP TRP ARG SEQRES 20 B 428 ILE ARG PRO LEU PRO GLU GLU MET LEU SER TYR ALA ARG SEQRES 21 B 428 ASP ASP THR HIS TYR LEU LEU TYR ILE TYR ASP LYS MET SEQRES 22 B 428 ARG LEU GLU MET TRP GLU ARG GLY ASN GLY GLN PRO VAL SEQRES 23 B 428 GLN LEU GLN VAL VAL TRP GLN ARG SER ARG ASP ILE CYS SEQRES 24 B 428 LEU LYS LYS PHE ILE LYS PRO ILE PHE THR ASP GLU SER SEQRES 25 B 428 TYR LEU GLU LEU TYR ARG LYS GLN LYS LYS HIS LEU ASN SEQRES 26 B 428 THR GLN GLN LEU THR ALA PHE GLN LEU LEU PHE ALA TRP SEQRES 27 B 428 ARG ASP LYS THR ALA ARG ARG GLU ASP GLU SER TYR GLY SEQRES 28 B 428 TYR VAL LEU PRO ASN HIS MET MET LEU LYS ILE ALA GLU SEQRES 29 B 428 GLU LEU PRO LYS GLU PRO GLN GLY ILE ILE ALA CYS CYS SEQRES 30 B 428 ASN PRO VAL PRO PRO LEU VAL ARG GLN GLN ILE ASN GLU SEQRES 31 B 428 MET HIS LEU LEU ILE GLN GLN ALA ARG GLU MET PRO LEU SEQRES 32 B 428 LEU LYS SER GLU VAL ALA ALA GLY VAL LYS LYS SER GLY SEQRES 33 B 428 PRO LEU PRO SER ALA GLU ARG LEU GLU ASN VAL LEU HET MG A 2 1 HET YT3 A 1 1 HET MG B 1 1 HET YT3 B 2 1 HETNAM MG MAGNESIUM ION HETNAM YT3 YTTRIUM (III) ION FORMUL 3 MG 2(MG 2+) FORMUL 4 YT3 2(Y 3+) FORMUL 7 HOH *252(H2 O) HELIX 1 1 ARG A 182 PHE A 187 5 6 HELIX 2 2 PRO A 213 ARG A 221 5 9 HELIX 3 3 TYR A 258 HIS A 264 1 7 HELIX 4 4 ALA A 268 GLN A 273 1 6 HELIX 5 5 PRO A 282 THR A 286 5 5 HELIX 6 6 SER A 293 LEU A 305 1 13 HELIX 7 7 LEU A 345 ILE A 351 5 7 HELIX 8 8 LEU A 352 THR A 357 1 6 HELIX 9 9 ALA A 368 GLY A 380 1 13 HELIX 10 10 THR A 389 LEU A 396 1 8 HELIX 11 11 SER A 402 ASN A 412 1 11 HELIX 12 12 PRO A 430 TYR A 443 1 14 HELIX 13 13 TYR A 443 GLY A 459 1 17 HELIX 14 14 PRO A 463 CYS A 477 1 15 HELIX 15 15 GLU A 489 TYR A 491 5 3 HELIX 16 16 LEU A 492 LYS A 497 1 6 HELIX 17 17 ASN A 503 ASP A 525 1 23 HELIX 18 18 SER A 527 LEU A 532 1 6 HELIX 19 19 PRO A 533 LEU A 544 1 12 HELIX 20 20 GLU A 547 ALA A 553 1 7 HELIX 21 21 PRO A 559 GLN A 565 1 7 HELIX 22 22 GLN A 565 GLU A 578 1 14 HELIX 23 23 LEU A 582 ALA A 587 1 6 HELIX 24 24 PRO B 213 SER B 217 5 5 HELIX 25 25 TYR B 258 HIS B 264 1 7 HELIX 26 26 ALA B 268 GLN B 273 1 6 HELIX 27 27 PRO B 282 THR B 286 5 5 HELIX 28 28 SER B 293 LEU B 305 1 13 HELIX 29 29 ASP B 348 ILE B 351 5 4 HELIX 30 30 LEU B 352 THR B 357 1 6 HELIX 31 31 ALA B 368 GLY B 380 1 13 HELIX 32 32 THR B 389 LEU B 396 1 8 HELIX 33 33 SER B 402 CYS B 411 1 10 HELIX 34 34 PRO B 430 TYR B 443 1 14 HELIX 35 35 TYR B 443 GLY B 459 1 17 HELIX 36 36 PRO B 463 LEU B 478 1 16 HELIX 37 37 THR B 487 GLU B 493 5 7 HELIX 38 38 TYR B 495 LYS B 499 5 5 HELIX 39 39 ASN B 503 ASP B 525 1 23 HELIX 40 40 SER B 527 LEU B 532 1 6 HELIX 41 41 PRO B 533 LEU B 544 1 12 HELIX 42 42 GLU B 547 CYS B 555 1 9 HELIX 43 43 PRO B 559 GLN B 565 1 7 HELIX 44 44 GLN B 565 GLU B 578 1 14 HELIX 45 45 LEU B 582 ALA B 587 1 6 SHEET 1 A 6 CYS A 288 ILE A 291 0 SHEET 2 A 6 ASP A 337 ASP A 341 1 O ILE A 339 N HIS A 289 SHEET 3 A 6 LEU A 325 SER A 332 -1 N ILE A 331 O PHE A 338 SHEET 4 A 6 GLU A 309 HIS A 317 -1 N ASN A 313 O GLN A 330 SHEET 5 A 6 VAL A 362 PHE A 365 1 O VAL A 364 N PHE A 310 SHEET 6 A 6 MET A 386 ASP A 388 1 O PHE A 387 N LYS A 363 SHEET 1 B 6 CYS B 288 ILE B 291 0 SHEET 2 B 6 ASP B 337 ASP B 341 1 O ILE B 339 N HIS B 289 SHEET 3 B 6 LEU B 325 SER B 332 -1 N ILE B 331 O PHE B 338 SHEET 4 B 6 GLU B 309 HIS B 317 -1 N HIS B 317 O LEU B 325 SHEET 5 B 6 VAL B 362 PHE B 365 1 O VAL B 364 N PHE B 310 SHEET 6 B 6 MET B 386 ASP B 388 1 O PHE B 387 N LYS B 363 LINK Y YT3 A 1 OD2 ASP A 488 1555 1555 2.84 LINK Y YT3 A 1 OD1 ASP A 488 1555 1555 2.86 LINK Y YT3 A 1 OE1 GLU A 489 1555 1555 2.60 LINK MG MG A 2 O HOH A 31 1555 1555 2.56 LINK MG MG A 2 O HOH A 38 1555 1555 2.49 LINK MG MG A 2 O HOH A 74 1555 1555 2.57 LINK MG MG A 2 OD1 ASN A 313 1555 1555 2.60 LINK MG MG B 1 O HOH B 165 1555 1555 2.42 LINK MG MG B 1 OD1 ASN B 313 1555 1555 2.81 LINK MG MG B 1 O HOH B 647 1555 1555 2.00 LINK MG MG B 1 O HOH B 648 1555 1555 2.02 LINK Y YT3 B 2 OD1 ASP B 488 1555 1555 2.53 LINK Y YT3 B 2 OD2 ASP B 488 1555 1555 3.27 LINK Y YT3 B 2 OE2 GLU B 489 1555 1555 2.08 LINK Y YT3 B 2 OE1 GLU B 489 1555 1555 2.40 CISPEP 1 ARG A 427 PRO A 428 0 -0.05 CISPEP 2 ASN A 556 PRO A 557 0 0.00 CISPEP 3 ARG B 427 PRO B 428 0 -0.09 CISPEP 4 ASN B 556 PRO B 557 0 -0.03 SITE 1 AC1 4 HOH A 31 HOH A 38 HOH A 74 ASN A 313 SITE 1 AC2 4 GLU A 296 GLU A 299 ASP A 488 GLU A 489 SITE 1 AC3 6 HOH B 165 ASN B 313 HIS B 366 ASP B 371 SITE 2 AC3 6 HOH B 647 HOH B 648 SITE 1 AC4 4 GLU B 296 GLU B 299 ASP B 488 GLU B 489 CRYST1 138.900 138.900 58.400 90.00 90.00 90.00 P 4 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 0.007199 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007199 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017123 0.00000