HEADER PROTEIN BINDING 31-MAY-19 6RVE TITLE CO-SUBSTITUTED BETA-KEGGIN BOUND TO PROTEINASE K SOLVED BY MR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEINASE K; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENDOPEPTIDASE K,TRITIRACHIUM ALKALINE PROTEINASE; COMPND 5 EC: 3.4.21.64 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARENGYODONTIUM ALBUM; SOURCE 3 ORGANISM_TAXID: 37998 KEYWDS POLYOXOMETALATE, COMPLEX, ALPHA-KEGGIN, PROTEINASE K, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.BREIBECK,A.BIJELIC,A.ROMPEL REVDAT 5 24-JAN-24 6RVE 1 REMARK REVDAT 4 15-NOV-23 6RVE 1 LINK ATOM REVDAT 3 20-NOV-19 6RVE 1 LINK REVDAT 2 02-OCT-19 6RVE 1 JRNL REVDAT 1 18-SEP-19 6RVE 0 JRNL AUTH J.BREIBECK,A.BIJELIC,A.ROMPEL JRNL TITL TRANSITION METAL-SUBSTITUTED KEGGIN POLYOXOTUNGSTATES JRNL TITL 2 ENABLING COVALENT ATTACHMENT TO PROTEINASE K UPON JRNL TITL 3 CO-CRYSTALLIZATION. JRNL REF CHEM.COMMUN.(CAMB.) V. 55 11519 2019 JRNL REFN ESSN 1364-548X JRNL PMID 31490500 JRNL DOI 10.1039/C9CC05818D REMARK 2 REMARK 2 RESOLUTION. 1.15 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.870 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 169670 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 8509 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 35.8513 - 3.5722 1.00 5442 296 0.1746 0.1793 REMARK 3 2 3.5722 - 2.8357 1.00 5423 284 0.1641 0.1862 REMARK 3 3 2.8357 - 2.4774 1.00 5445 293 0.1649 0.2083 REMARK 3 4 2.4774 - 2.2509 1.00 5417 287 0.1573 0.1879 REMARK 3 5 2.2509 - 2.0896 1.00 5473 283 0.1440 0.1946 REMARK 3 6 2.0896 - 1.9664 1.00 5447 288 0.1423 0.1849 REMARK 3 7 1.9664 - 1.8679 1.00 5444 275 0.1454 0.2114 REMARK 3 8 1.8679 - 1.7866 1.00 5447 283 0.1504 0.2048 REMARK 3 9 1.7866 - 1.7178 1.00 5439 290 0.1556 0.1950 REMARK 3 10 1.7178 - 1.6586 1.00 5470 288 0.1592 0.1923 REMARK 3 11 1.6586 - 1.6067 1.00 5405 282 0.1648 0.1847 REMARK 3 12 1.6067 - 1.5608 1.00 5442 290 0.1737 0.2202 REMARK 3 13 1.5608 - 1.5197 1.00 5447 283 0.1929 0.2081 REMARK 3 14 1.5197 - 1.4826 1.00 5406 286 0.1996 0.2408 REMARK 3 15 1.4826 - 1.4489 1.00 5499 291 0.2148 0.2314 REMARK 3 16 1.4489 - 1.4181 1.00 5409 285 0.2240 0.2478 REMARK 3 17 1.4181 - 1.3897 1.00 5434 287 0.2399 0.2574 REMARK 3 18 1.3897 - 1.3635 1.00 5446 288 0.2520 0.2751 REMARK 3 19 1.3635 - 1.3391 1.00 5438 286 0.2779 0.2746 REMARK 3 20 1.3391 - 1.3164 1.00 5443 292 0.2888 0.3326 REMARK 3 21 1.3164 - 1.2952 1.00 5439 286 0.3090 0.3327 REMARK 3 22 1.2952 - 1.2753 1.00 5453 284 0.3317 0.3896 REMARK 3 23 1.2753 - 1.2565 1.00 5420 284 0.3402 0.3599 REMARK 3 24 1.2565 - 1.2388 1.00 5465 288 0.3508 0.3899 REMARK 3 25 1.2388 - 1.2221 0.99 5366 286 0.3690 0.3751 REMARK 3 26 1.2221 - 1.2062 0.98 5330 283 0.3808 0.4101 REMARK 3 27 1.2062 - 1.1911 0.97 5314 270 0.3911 0.3843 REMARK 3 28 1.1911 - 1.1768 0.94 5090 272 0.4132 0.3850 REMARK 3 29 1.1768 - 1.1631 0.90 4891 263 0.4253 0.4448 REMARK 3 30 1.1631 - 1.1500 0.84 4577 256 0.4292 0.4392 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.320 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 : 0.019 2297 REMARK 3 ANGLE : 2.903 3498 REMARK 3 CHIRALITY : 0.098 311 REMARK 3 PLANARITY : 0.010 370 REMARK 3 DIHEDRAL : 13.990 723 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 6RVE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1292102648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 169779 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 35.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.16950 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1IC6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE (PH 4.5), 0.3 REMARK 280 -0.7 M AMMONIUM ACETATE, 0.5 M BETAINE, 10 MM CO-SUBSTITUTED REMARK 280 BETA-KEGGIN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 53.33500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.21000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 80.00250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.21000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.21000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.66750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.21000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.21000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 80.00250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.21000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.21000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.66750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.33500 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 TOTAL BURIED SURFACE AREA: 430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 A 521 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 700 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 GLN A 278 REMARK 465 ALA A 279 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 H SER A 45 O5 XCO A 301 0.66 REMARK 500 SG CYS A 178 HG CYS A 249 1.01 REMARK 500 SG CYS A 34 HG CYS A 123 1.11 REMARK 500 O HOH A 434 O HOH A 668 1.55 REMARK 500 O HOH A 472 O HOH A 659 1.71 REMARK 500 O HOH A 461 O HOH A 568 1.77 REMARK 500 O2 XCO A 301 O HOH A 401 1.78 REMARK 500 OE1 GLN A 103 O HOH A 402 1.82 REMARK 500 O HOH A 637 O HOH A 761 1.85 REMARK 500 O28 XCO A 301 O HOH A 403 1.87 REMARK 500 O HOH A 543 O HOH A 571 1.90 REMARK 500 O HOH A 459 O HOH A 749 1.90 REMARK 500 O HOH A 410 O HOH A 517 1.90 REMARK 500 O HOH A 699 O HOH A 765 1.92 REMARK 500 O HOH A 591 O HOH A 648 1.93 REMARK 500 O HOH A 499 O HOH A 682 1.95 REMARK 500 O HOH A 654 O HOH A 704 1.95 REMARK 500 O HOH A 402 O HOH A 620 1.97 REMARK 500 O HOH A 420 O HOH A 651 1.98 REMARK 500 O HOH A 584 O HOH A 698 2.02 REMARK 500 O HOH A 403 O HOH A 621 2.03 REMARK 500 O HOH A 626 O HOH A 732 2.05 REMARK 500 O HOH A 497 O HOH A 670 2.06 REMARK 500 OD1 ASP A 112 O HOH A 404 2.07 REMARK 500 O HOH A 626 O HOH A 753 2.07 REMARK 500 O2 KCO A 302 O HOH A 405 2.07 REMARK 500 O HOH A 467 O HOH A 585 2.08 REMARK 500 O HOH A 430 O HOH A 588 2.10 REMARK 500 O9 KCO A 302 O HOH A 406 2.12 REMARK 500 O10 XCO A 301 O HOH A 403 2.12 REMARK 500 O16 XCO A 301 O HOH A 401 2.13 REMARK 500 O10 XCO A 301 O HOH A 403 2.14 REMARK 500 O33 XCO A 301 O HOH A 407 2.15 REMARK 500 O HOH A 686 O HOH A 714 2.16 REMARK 500 OD2 ASP A 207 O30 KCO A 302 2.17 REMARK 500 O HOH A 447 O HOH A 678 2.17 REMARK 500 O HOH A 571 O HOH A 721 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HZ1 LYS A 258 O2 XCO A 301 8765 0.45 REMARK 500 HZ1 LYS A 258 O17 XCO A 301 8765 1.38 REMARK 500 HZ2 LYS A 258 W3 XCO A 301 8765 1.39 REMARK 500 HZ2 LYS A 258 O17 XCO A 301 8765 1.44 REMARK 500 NZ LYS A 258 O17 XCO A 301 8765 1.71 REMARK 500 O HOH A 447 O HOH A 508 3644 1.85 REMARK 500 O HOH A 666 O HOH A 681 4465 2.11 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 LYS A 258 CD LYS A 258 CE -0.290 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 188 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 LYS A 258 CG - CD - CE ANGL. DEV. = -19.4 DEGREES REMARK 500 LYS A 258 CD - CE - NZ ANGL. DEV. = -31.8 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 ASP A 39 -148.34 -165.92 REMARK 500 ASN A 270 77.07 -112.35 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 KCO A 302 W12 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 207 OD1 REMARK 620 2 KCO A 302 O12 67.8 REMARK 620 3 KCO A 302 O31 83.4 102.9 REMARK 620 4 KCO A 302 O32 149.7 83.1 95.6 REMARK 620 5 KCO A 302 O35 106.6 91.2 165.2 81.2 REMARK 620 6 KCO A 302 O40 135.1 152.0 70.3 71.0 95.1 REMARK 620 7 ASP A 207 OD2 42.9 110.6 73.3 163.7 106.3 93.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 KCO A 302 CO1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 207 OD2 REMARK 620 2 KCO A 302 O29 153.2 REMARK 620 3 KCO A 302 O30 68.3 88.7 REMARK 620 4 KCO A 302 O34 115.6 89.9 166.6 REMARK 620 5 KCO A 302 O39 104.6 78.7 70.2 96.4 REMARK 620 6 HOH A 417 O 92.5 82.8 111.2 81.9 161.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 W2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 258 NZ REMARK 620 2 XCO A 301 O16 99.6 REMARK 620 3 XCO A 301 O17 56.7 43.0 REMARK 620 4 XCO A 301 O18 141.1 45.3 86.3 REMARK 620 5 XCO A 301 O19 136.8 90.3 119.1 49.2 REMARK 620 6 XCO A 301 O2 120.0 50.3 80.0 56.0 98.7 REMARK 620 7 XCO A 301 O37 94.1 45.3 55.3 50.8 63.9 92.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 W3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 258 NZ REMARK 620 2 XCO A 301 O13 121.7 REMARK 620 3 XCO A 301 O17 62.0 81.6 REMARK 620 4 XCO A 301 O20 71.9 161.3 95.9 REMARK 620 5 XCO A 301 O21 141.5 87.0 155.1 87.8 REMARK 620 6 XCO A 301 O3 82.7 94.4 133.9 100.4 68.8 REMARK 620 7 XCO A 301 O37 124.8 75.7 71.4 85.9 84.3 152.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 W3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 258 NZ REMARK 620 2 XCO A 301 O13 107.2 REMARK 620 3 XCO A 301 O17 60.7 61.6 REMARK 620 4 XCO A 301 O20 86.3 136.5 93.5 REMARK 620 5 XCO A 301 O21 172.5 71.1 122.5 99.9 REMARK 620 6 XCO A 301 O3 99.3 77.7 122.1 142.1 73.3 REMARK 620 7 XCO A 301 O37 114.2 58.1 57.0 78.6 71.4 130.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 W1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 401 O REMARK 620 2 XCO A 301 O1 105.4 REMARK 620 3 XCO A 301 O13 162.7 77.8 REMARK 620 4 XCO A 301 O14 84.8 60.1 110.8 REMARK 620 5 XCO A 301 O15 135.9 55.4 60.1 51.0 REMARK 620 6 XCO A 301 O16 23.5 83.4 159.0 66.2 115.5 REMARK 620 7 XCO A 301 O37 103.6 119.9 88.9 71.6 67.1 108.7 REMARK 620 8 HOH A 411 O 74.9 102.3 87.8 148.7 142.6 87.3 135.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 W2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 401 O REMARK 620 2 XCO A 301 O16 59.6 REMARK 620 3 XCO A 301 O17 116.7 83.0 REMARK 620 4 XCO A 301 O18 71.9 87.4 160.3 REMARK 620 5 XCO A 301 O19 137.7 158.6 94.7 88.0 REMARK 620 6 XCO A 301 O2 51.1 97.5 91.9 106.5 103.8 REMARK 620 7 XCO A 301 O37 130.2 76.1 75.6 85.4 82.7 166.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 W10 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 403 O REMARK 620 2 XCO A 301 O10 60.0 REMARK 620 3 XCO A 301 O28 49.9 102.3 REMARK 620 4 XCO A 301 O33 71.8 100.4 87.0 REMARK 620 5 XCO A 301 O34 120.3 97.0 92.1 162.4 REMARK 620 6 XCO A 301 O35 137.4 96.0 159.2 80.0 95.4 REMARK 620 7 XCO A 301 O38 108.0 164.7 72.5 65.3 97.6 87.3 REMARK 620 8 HOH A 407 O 88.6 76.3 125.4 42.0 142.5 49.9 94.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 W10 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 403 O REMARK 620 2 XCO A 301 O10 42.9 REMARK 620 3 XCO A 301 O28 35.3 76.9 REMARK 620 4 XCO A 301 O33 52.9 61.8 71.6 REMARK 620 5 XCO A 301 O34 108.4 72.9 125.0 126.4 REMARK 620 6 XCO A 301 O35 89.7 59.7 121.7 54.8 78.9 REMARK 620 7 XCO A 301 O38 100.8 117.3 93.3 56.6 141.4 76.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 CO1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 468 O REMARK 620 2 XCO A 301 O29 93.2 REMARK 620 3 XCO A 301 O30 83.1 93.9 REMARK 620 4 XCO A 301 O34 103.7 92.3 170.6 REMARK 620 5 XCO A 301 O36 98.1 168.6 89.0 83.6 REMARK 620 6 XCO A 301 O39 153.5 77.8 72.8 101.6 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 XCO A 301 CO1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 468 O REMARK 620 2 XCO A 301 O29 81.1 REMARK 620 3 XCO A 301 O30 104.9 98.8 REMARK 620 4 XCO A 301 O34 81.4 65.6 162.4 REMARK 620 5 XCO A 301 O36 100.8 129.5 128.1 64.9 REMARK 620 6 XCO A 301 O39 149.5 69.0 85.7 81.2 94.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 KCO A 302 W9 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 406 O REMARK 620 2 KCO A 302 O15 114.3 REMARK 620 3 KCO A 302 O23 73.6 78.8 REMARK 620 4 KCO A 302 O27 125.3 99.1 158.7 REMARK 620 5 KCO A 302 O33 78.1 161.3 92.4 83.1 REMARK 620 6 KCO A 302 O38 135.1 86.3 72.2 86.5 75.3 REMARK 620 7 KCO A 302 O9 38.9 94.9 101.9 99.5 103.1 173.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XCO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KCO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BET A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6RUK RELATED DB: PDB REMARK 900 RELATED ID: 6RUH RELATED DB: PDB REMARK 900 RELATED ID: 6RUG RELATED DB: PDB REMARK 900 RELATED ID: 6RUN RELATED DB: PDB REMARK 900 RELATED ID: 6RUW RELATED DB: PDB DBREF 6RVE A 1 279 UNP P06873 PRTK_PARAQ 106 384 SEQADV 6RVE ASP A 207 UNP P06873 SER 312 CONFLICT SEQRES 1 A 279 ALA ALA GLN THR ASN ALA PRO TRP GLY LEU ALA ARG ILE SEQRES 2 A 279 SER SER THR SER PRO GLY THR SER THR TYR TYR TYR ASP SEQRES 3 A 279 GLU SER ALA GLY GLN GLY SER CYS VAL TYR VAL ILE ASP SEQRES 4 A 279 THR GLY ILE GLU ALA SER HIS PRO GLU PHE GLU GLY ARG SEQRES 5 A 279 ALA GLN MET VAL LYS THR TYR TYR TYR SER SER ARG ASP SEQRES 6 A 279 GLY ASN GLY HIS GLY THR HIS CYS ALA GLY THR VAL GLY SEQRES 7 A 279 SER ARG THR TYR GLY VAL ALA LYS LYS THR GLN LEU PHE SEQRES 8 A 279 GLY VAL LYS VAL LEU ASP ASP ASN GLY SER GLY GLN TYR SEQRES 9 A 279 SER THR ILE ILE ALA GLY MET ASP PHE VAL ALA SER ASP SEQRES 10 A 279 LYS ASN ASN ARG ASN CYS PRO LYS GLY VAL VAL ALA SER SEQRES 11 A 279 LEU SER LEU GLY GLY GLY TYR SER SER SER VAL ASN SER SEQRES 12 A 279 ALA ALA ALA ARG LEU GLN SER SER GLY VAL MET VAL ALA SEQRES 13 A 279 VAL ALA ALA GLY ASN ASN ASN ALA ASP ALA ARG ASN TYR SEQRES 14 A 279 SER PRO ALA SER GLU PRO SER VAL CYS THR VAL GLY ALA SEQRES 15 A 279 SER ASP ARG TYR ASP ARG ARG SER SER PHE SER ASN TYR SEQRES 16 A 279 GLY SER VAL LEU ASP ILE PHE GLY PRO GLY THR ASP ILE SEQRES 17 A 279 LEU SER THR TRP ILE GLY GLY SER THR ARG SER ILE SER SEQRES 18 A 279 GLY THR SER MET ALA THR PRO HIS VAL ALA GLY LEU ALA SEQRES 19 A 279 ALA TYR LEU MET THR LEU GLY LYS THR THR ALA ALA SER SEQRES 20 A 279 ALA CYS ARG TYR ILE ALA ASP THR ALA ASN LYS GLY ASP SEQRES 21 A 279 LEU SER ASN ILE PRO PHE GLY THR VAL ASN LEU LEU ALA SEQRES 22 A 279 TYR ASN ASN TYR GLN ALA HET XCO A 301 104 HET KCO A 302 51 HET SO4 A 303 5 HET BET A 304 19 HETNAM XCO CO-SUBSTITUTED BETA-KEGGIN HETNAM KCO CO-SUBSTITUTED BETA-KEGGIN HETNAM SO4 SULFATE ION HETNAM BET TRIMETHYL GLYCINE FORMUL 2 XCO CO O39 SI W11 FORMUL 3 KCO CO O38 SI W11 FORMUL 4 SO4 O4 S 2- FORMUL 5 BET C5 H12 N O2 1+ FORMUL 6 HOH *390(H2 O) HELIX 1 AA1 PRO A 7 SER A 14 1 8 HELIX 2 AA2 HIS A 46 GLU A 50 5 5 HELIX 3 AA3 GLY A 68 SER A 79 1 12 HELIX 4 AA4 GLN A 103 LYS A 118 1 16 HELIX 5 AA5 ASN A 119 ARG A 121 5 3 HELIX 6 AA6 SER A 138 SER A 151 1 14 HELIX 7 AA7 ASP A 165 ARG A 167 5 3 HELIX 8 AA8 GLY A 222 LEU A 240 1 19 HELIX 9 AA9 SER A 247 ALA A 256 1 10 SHEET 1 AA1 2 ALA A 2 GLN A 3 0 SHEET 2 AA1 2 TYR A 23 TYR A 24 -1 O TYR A 23 N GLN A 3 SHEET 1 AA2 7 ALA A 53 THR A 58 0 SHEET 2 AA2 7 GLN A 89 LYS A 94 1 O GLY A 92 N VAL A 56 SHEET 3 AA2 7 SER A 33 ASP A 39 1 N VAL A 37 O PHE A 91 SHEET 4 AA2 7 GLY A 126 LEU A 131 1 O SER A 130 N TYR A 36 SHEET 5 AA2 7 MET A 154 ALA A 158 1 O MET A 154 N ALA A 129 SHEET 6 AA2 7 CYS A 178 SER A 183 1 O CYS A 178 N VAL A 157 SHEET 7 AA2 7 ILE A 201 PRO A 204 1 O ILE A 201 N GLY A 181 SHEET 1 AA3 2 GLY A 135 GLY A 136 0 SHEET 2 AA3 2 TYR A 169 SER A 170 -1 O SER A 170 N GLY A 135 SHEET 1 AA4 2 ILE A 208 TRP A 212 0 SHEET 2 AA4 2 SER A 216 ILE A 220 -1 O ILE A 220 N ILE A 208 SHEET 1 AA5 2 ASN A 257 LYS A 258 0 SHEET 2 AA5 2 LEU A 271 LEU A 272 -1 O LEU A 272 N ASN A 257 SSBOND 1 CYS A 34 CYS A 123 1555 1555 2.06 SSBOND 2 CYS A 178 CYS A 249 1555 1555 2.09 LINK N SER A 45 O5 BXCO A 301 1555 1555 1.38 LINK NZ LYS A 258 O2 BXCO A 301 1555 8765 1.34 LINK OD1 ASP A 207 W12 KCO A 302 1555 1555 2.74 LINK OD2 ASP A 207 CO1 KCO A 302 1555 1555 1.87 LINK OD2 ASP A 207 W12 KCO A 302 1555 1555 3.02 LINK NZ LYS A 258 W2 BXCO A 301 1555 8765 2.83 LINK NZ LYS A 258 W3 AXCO A 301 1555 8765 2.53 LINK NZ LYS A 258 W3 BXCO A 301 1555 8765 2.28 LINK W1 BXCO A 301 O HOH A 401 1555 1555 3.08 LINK W2 AXCO A 301 O HOH A 401 1555 1555 2.26 LINK W10AXCO A 301 O HOH A 403 1555 1555 2.36 LINK W10BXCO A 301 O HOH A 403 1555 1555 2.97 LINK W10AXCO A 301 O HOH A 407 1555 1555 3.18 LINK W1 BXCO A 301 O HOH A 411 1555 1555 3.20 LINK CO1 AXCO A 301 O HOH A 468 1555 1555 2.11 LINK CO1 BXCO A 301 O HOH A 468 1555 1555 2.13 LINK W9 KCO A 302 O HOH A 406 1555 1555 3.21 LINK CO1 KCO A 302 O HOH A 417 1555 1555 2.23 CISPEP 1 SER A 170 PRO A 171 0 2.09 SITE 1 AC1 22 ILE A 42 GLU A 43 ALA A 44 SER A 45 SITE 2 AC1 22 MET A 55 SER A 62 SER A 63 ARG A 64 SITE 3 AC1 22 LYS A 258 GLY A 259 HOH A 401 HOH A 403 SITE 4 AC1 22 HOH A 407 HOH A 411 HOH A 412 HOH A 414 SITE 5 AC1 22 HOH A 418 HOH A 427 HOH A 437 HOH A 468 SITE 6 AC1 22 HOH A 614 HOH A 621 SITE 1 AC2 16 SER A 140 ARG A 185 TYR A 186 ASP A 207 SITE 2 AC2 16 THR A 244 ALA A 245 ALA A 246 HOH A 405 SITE 3 AC2 16 HOH A 406 HOH A 409 HOH A 417 HOH A 424 SITE 4 AC2 16 HOH A 431 HOH A 499 HOH A 628 HOH A 643 SITE 1 AC3 7 PRO A 7 TRP A 8 ARG A 185 HOH A 483 SITE 2 AC3 7 HOH A 487 HOH A 532 HOH A 634 SITE 1 AC4 6 HIS A 69 ASN A 161 SER A 221 GLY A 222 SITE 2 AC4 6 SER A 224 HOH A 518 CRYST1 68.420 68.420 106.670 90.00 90.00 90.00 P 43 21 2 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 0.014616 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014616 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009375 0.00000