HEADER LIGASE 04-JUL-12 4B0T TITLE STRUCTURE OF THE PUP LIGASE PAFA OF THE PROKARYOTIC UBIQUITIN-LIKE TITLE 2 MODIFICATION PATHWAY IN COMPLEX WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUP--PROTEIN LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PAFA, PROTEASOME ACCESSORY FACTOR A, PUP-CONJUGATING ENZYME; COMPND 5 EC: 6.3.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM; SOURCE 3 ORGANISM_TAXID: 1718; SOURCE 4 ATCC: 13032; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET EXPRESSION SYSTEM KEYWDS LIGASE, PUPYLATION, DEPUPYLATION, PROKARYOTIC UBIQUITIN-LIKE PROTEIN, KEYWDS 2 PROTEASOME EXPDTA X-RAY DIFFRACTION AUTHOR D.OZCELIK,J.BARANDUN,N.SCHMITZ,M.SUTTER,E.GUTH,F.F.DAMBERGER,F.H.- AUTHOR 2 T.ALLAIN,N.BAN,E.WEBER-BAN REVDAT 2 08-MAY-24 4B0T 1 REMARK LINK REVDAT 1 12-SEP-12 4B0T 0 JRNL AUTH D.OZCELIK,J.BARANDUN,N.SCHMITZ,M.SUTTER,E.GUTH, JRNL AUTH 2 F.F.DAMBERGER,F.H.-T.ALLAIN,N.BAN,E.WEBER-BAN JRNL TITL STRUCTURES OF PUP LIGASE PAFA AND DEPUPYLASE DOP FROM THE JRNL TITL 2 PROKARYOTIC UBIQUITIN-LIKE MODIFICATION PATHWAY. JRNL REF NAT.COMMUN. V. 3 1014 2012 JRNL REFN ESSN 2041-1723 JRNL PMID 22910360 JRNL DOI 10.1038/NCOMMS2009 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 64620 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3274 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 49.4295 - 6.1373 0.97 2874 124 0.1595 0.1829 REMARK 3 2 6.1373 - 4.8727 0.99 2747 162 0.1568 0.1795 REMARK 3 3 4.8727 - 4.2572 0.97 2678 152 0.1324 0.1700 REMARK 3 4 4.2572 - 3.8681 0.99 2712 135 0.1463 0.1957 REMARK 3 5 3.8681 - 3.5909 1.00 2714 151 0.1699 0.2128 REMARK 3 6 3.5909 - 3.3793 0.99 2713 150 0.1876 0.2248 REMARK 3 7 3.3793 - 3.2101 0.97 2646 120 0.2010 0.2508 REMARK 3 8 3.2101 - 3.0703 0.99 2688 139 0.1964 0.2623 REMARK 3 9 3.0703 - 2.9522 1.00 2699 152 0.2012 0.2395 REMARK 3 10 2.9522 - 2.8503 1.00 2684 133 0.1954 0.2528 REMARK 3 11 2.8503 - 2.7612 1.00 2689 152 0.1905 0.2449 REMARK 3 12 2.7612 - 2.6823 1.00 2652 146 0.1910 0.2312 REMARK 3 13 2.6823 - 2.6117 1.00 2694 145 0.1913 0.2117 REMARK 3 14 2.6117 - 2.5479 0.99 2680 133 0.2086 0.2763 REMARK 3 15 2.5479 - 2.4900 0.98 2596 131 0.2090 0.2776 REMARK 3 16 2.4900 - 2.4370 1.00 2699 134 0.2052 0.2735 REMARK 3 17 2.4370 - 2.3883 1.00 2644 151 0.1946 0.2498 REMARK 3 18 2.3883 - 2.3432 1.00 2672 163 0.2113 0.2530 REMARK 3 19 2.3432 - 2.3014 1.00 2634 145 0.2180 0.2629 REMARK 3 20 2.3014 - 2.2624 1.00 2680 166 0.2337 0.2970 REMARK 3 21 2.2624 - 2.2259 1.00 2649 150 0.2318 0.2835 REMARK 3 22 2.2259 - 2.1916 1.00 2696 121 0.2550 0.3123 REMARK 3 23 2.1916 - 2.1594 0.83 2206 119 0.2571 0.3177 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 : 0.33 REMARK 3 B_SOL : 50.13 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.59430 REMARK 3 B22 (A**2) : -6.77660 REMARK 3 B33 (A**2) : 5.18230 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 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 : 0.008 7616 REMARK 3 ANGLE : 1.202 10340 REMARK 3 CHIRALITY : 0.091 1168 REMARK 3 PLANARITY : 0.006 1336 REMARK 3 DIHEDRAL : 14.446 2856 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 2:48) REMARK 3 ORIGIN FOR THE GROUP (A): 13.4577 34.2745 38.3596 REMARK 3 T TENSOR REMARK 3 T11: 0.3837 T22: 0.3842 REMARK 3 T33: 0.3784 T12: -0.0351 REMARK 3 T13: 0.0971 T23: -0.0424 REMARK 3 L TENSOR REMARK 3 L11: 0.0809 L22: 0.5773 REMARK 3 L33: 0.1860 L12: -0.2811 REMARK 3 L13: -0.2188 L23: 0.4335 REMARK 3 S TENSOR REMARK 3 S11: -0.0405 S12: 0.0630 S13: -0.0775 REMARK 3 S21: 0.0904 S22: 0.0966 S23: -0.0111 REMARK 3 S31: -0.0021 S32: 0.0895 S33: 0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 49:477) REMARK 3 ORIGIN FOR THE GROUP (A): 20.7421 10.5568 5.3873 REMARK 3 T TENSOR REMARK 3 T11: 0.2278 T22: 0.3114 REMARK 3 T33: 0.2581 T12: -0.0350 REMARK 3 T13: 0.0453 T23: 0.0420 REMARK 3 L TENSOR REMARK 3 L11: 0.9507 L22: 1.2528 REMARK 3 L33: 0.8750 L12: -0.2704 REMARK 3 L13: -0.1153 L23: -0.0068 REMARK 3 S TENSOR REMARK 3 S11: -0.1144 S12: 0.0224 S13: -0.1663 REMARK 3 S21: -0.0472 S22: 0.0393 S23: -0.0184 REMARK 3 S31: 0.0924 S32: -0.0650 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 2:78) REMARK 3 ORIGIN FOR THE GROUP (A): 19.0493 23.5414 22.9020 REMARK 3 T TENSOR REMARK 3 T11: 0.2629 T22: 0.3293 REMARK 3 T33: 0.3210 T12: -0.0298 REMARK 3 T13: -0.0044 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 0.3582 L22: 0.3987 REMARK 3 L33: 0.6977 L12: -0.1623 REMARK 3 L13: -0.6749 L23: -0.2620 REMARK 3 S TENSOR REMARK 3 S11: 0.0725 S12: -0.0916 S13: 0.0571 REMARK 3 S21: 0.0607 S22: -0.0126 S23: -0.0615 REMARK 3 S31: -0.1622 S32: 0.0478 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 79:336) REMARK 3 ORIGIN FOR THE GROUP (A): -0.6885 41.8593 46.0644 REMARK 3 T TENSOR REMARK 3 T11: 0.3504 T22: 0.2823 REMARK 3 T33: 0.3272 T12: -0.0135 REMARK 3 T13: 0.0673 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.6766 L22: 1.8755 REMARK 3 L33: 0.3473 L12: -0.6298 REMARK 3 L13: -0.1062 L23: 0.4737 REMARK 3 S TENSOR REMARK 3 S11: -0.0614 S12: 0.0816 S13: 0.1060 REMARK 3 S21: 0.2784 S22: 0.0291 S23: 0.1753 REMARK 3 S31: 0.0192 S32: 0.0237 S33: -0.0121 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 337:478) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1732 31.5078 46.3026 REMARK 3 T TENSOR REMARK 3 T11: 0.2974 T22: 0.2187 REMARK 3 T33: 0.2168 T12: 0.0186 REMARK 3 T13: -0.0823 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.3019 L22: 0.8068 REMARK 3 L33: 0.5446 L12: -0.3412 REMARK 3 L13: -0.6200 L23: -0.3336 REMARK 3 S TENSOR REMARK 3 S11: -0.1105 S12: -0.1020 S13: 0.0241 REMARK 3 S21: 0.3896 S22: 0.1014 S23: -0.2653 REMARK 3 S31: 0.1423 S32: 0.0931 S33: 0.0004 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 4B0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1290053150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI 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 : 65412 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 49.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.390 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.390 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER FOR MR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CHES-NAOH, PH 9.0 (278 K), 200 REMARK 280 MM LI2SO4 AND 22 % (V/V) PEG-4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 31.05000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.51000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.51000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.40500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 GLY A 26 REMARK 465 ASP A 27 REMARK 465 SER A 28 REMARK 465 LYS A 29 REMARK 465 LYS A 30 REMARK 465 LEU A 31 REMARK 465 GLU A 478 REMARK 465 SER A 479 REMARK 465 TYR A 480 REMARK 465 ARG A 481 REMARK 465 SER A 482 REMARK 465 LYS A 483 REMARK 465 SER A 484 REMARK 465 SER A 485 REMARK 465 VAL A 486 REMARK 465 GLU A 487 REMARK 465 HIS A 488 REMARK 465 HIS A 489 REMARK 465 HIS A 490 REMARK 465 HIS A 491 REMARK 465 HIS A 492 REMARK 465 HIS A 493 REMARK 465 MET B 1 REMARK 465 GLY B 26 REMARK 465 ASP B 27 REMARK 465 SER B 28 REMARK 465 LYS B 29 REMARK 465 LYS B 30 REMARK 465 SER B 479 REMARK 465 TYR B 480 REMARK 465 ARG B 481 REMARK 465 SER B 482 REMARK 465 LYS B 483 REMARK 465 SER B 484 REMARK 465 SER B 485 REMARK 465 VAL B 486 REMARK 465 GLU B 487 REMARK 465 HIS B 488 REMARK 465 HIS B 489 REMARK 465 HIS B 490 REMARK 465 HIS B 491 REMARK 465 HIS B 492 REMARK 465 HIS B 493 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 O3B ADP A 1478 O HOH A 2251 2.03 REMARK 500 NH1 ARG A 60 O1B ADP A 1478 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 197 -169.88 -100.12 REMARK 500 SER A 313 -137.21 50.18 REMARK 500 THR A 401 -168.63 -129.27 REMARK 500 MET B 229 -60.36 -97.91 REMARK 500 SER B 313 -136.57 56.54 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 MG B1480 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 16 OE1 REMARK 620 2 HOH A2016 O 89.8 REMARK 620 3 HOH A2017 O 64.7 103.2 REMARK 620 4 HOH A2018 O 78.6 167.4 67.6 REMARK 620 5 HOH A2235 O 164.0 96.7 127.2 95.8 REMARK 620 6 ADP B1479 O1B 83.1 90.8 144.4 92.6 82.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1479 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A1478 O1A REMARK 620 2 ADP A1478 O2B 26.1 REMARK 620 3 HOH A2053 O 106.9 80.9 REMARK 620 4 HOH A2063 O 155.4 163.1 93.3 REMARK 620 5 HOH A2250 O 65.7 91.8 172.6 94.0 REMARK 620 6 HOH A2251 O 80.6 87.2 101.5 109.5 77.1 REMARK 620 7 GLU B 16 OE1 79.1 81.9 100.4 83.6 79.2 153.6 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 ADP A 1478 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1479 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 1479 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1480 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4B0S RELATED DB: PDB REMARK 900 STRUCTURE OF THE DEAMIDASE-DEPUPYLASE DOP OF THE PROKARYOTIC REMARK 900 UBIQUITIN-LIKE MODIFICATION PATHWAY IN COMPLEX WITH ATP REMARK 900 RELATED ID: 4B0R RELATED DB: PDB REMARK 900 STRUCTURE OF THE DEAMIDASE-DEPUPYLASE DOP OF THE PROKARYOTIC REMARK 900 UBIQUITIN-LIKE MODIFICATION PATHWAY DBREF 4B0T A 1 482 UNP Q8NQE1 PAFA_CORGL 1 482 DBREF 4B0T B 1 482 UNP Q8NQE1 PAFA_CORGL 1 482 SEQADV 4B0T LYS A 483 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T SER A 484 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T SER A 485 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T VAL A 486 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T GLU A 487 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS A 488 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS A 489 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS A 490 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS A 491 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS A 492 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS A 493 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T LYS B 483 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T SER B 484 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T SER B 485 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T VAL B 486 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T GLU B 487 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS B 488 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS B 489 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS B 490 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS B 491 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS B 492 UNP Q8NQE1 EXPRESSION TAG SEQADV 4B0T HIS B 493 UNP Q8NQE1 EXPRESSION TAG SEQRES 1 A 493 MET SER THR VAL GLU SER ALA LEU THR ARG ARG ILE MET SEQRES 2 A 493 GLY ILE GLU THR GLU TYR GLY LEU THR PHE VAL ASP GLY SEQRES 3 A 493 ASP SER LYS LYS LEU ARG PRO ASP GLU ILE ALA ARG ARG SEQRES 4 A 493 MET PHE ARG PRO ILE VAL GLU LYS TYR SER SER SER ASN SEQRES 5 A 493 ILE PHE ILE PRO ASN GLY SER ARG LEU TYR LEU ASP VAL SEQRES 6 A 493 GLY SER HIS PRO GLU TYR ALA THR ALA GLU CYS ASP ASN SEQRES 7 A 493 LEU THR GLN LEU ILE ASN PHE GLU LYS ALA GLY ASP VAL SEQRES 8 A 493 ILE ALA ASP ARG MET ALA VAL ASP ALA GLU GLU SER LEU SEQRES 9 A 493 ALA LYS GLU ASP ILE ALA GLY GLN VAL TYR LEU PHE LYS SEQRES 10 A 493 ASN ASN VAL ASP SER VAL GLY ASN SER TYR GLY CYS HIS SEQRES 11 A 493 GLU ASN TYR LEU VAL GLY ARG SER MET PRO LEU LYS ALA SEQRES 12 A 493 LEU GLY LYS ARG LEU MET PRO PHE LEU ILE THR ARG GLN SEQRES 13 A 493 LEU ILE CYS GLY ALA GLY ARG ILE HIS HIS PRO ASN PRO SEQRES 14 A 493 LEU ASP LYS GLY GLU SER PHE PRO LEU GLY TYR CYS ILE SEQRES 15 A 493 SER GLN ARG SER ASP HIS VAL TRP GLU GLY VAL SER SER SEQRES 16 A 493 ALA THR THR ARG SER ARG PRO ILE ILE ASN THR ARG ASP SEQRES 17 A 493 GLU PRO HIS ALA ASP SER HIS SER TYR ARG ARG LEU HIS SEQRES 18 A 493 VAL ILE VAL GLY ASP ALA ASN MET ALA GLU PRO SER ILE SEQRES 19 A 493 ALA LEU LYS VAL GLY SER THR LEU LEU VAL LEU GLU MET SEQRES 20 A 493 ILE GLU ALA ASP PHE GLY LEU PRO SER LEU GLU LEU ALA SEQRES 21 A 493 ASN ASP ILE ALA SER ILE ARG GLU ILE SER ARG ASP ALA SEQRES 22 A 493 THR GLY SER THR LEU LEU SER LEU LYS ASP GLY THR THR SEQRES 23 A 493 MET THR ALA LEU GLN ILE GLN GLN VAL VAL PHE GLU HIS SEQRES 24 A 493 ALA SER LYS TRP LEU GLU GLN ARG PRO GLU PRO GLU PHE SEQRES 25 A 493 SER GLY THR SER ASN THR GLU MET ALA ARG VAL LEU ASP SEQRES 26 A 493 LEU TRP GLY ARG MET LEU LYS ALA ILE GLU SER GLY ASP SEQRES 27 A 493 PHE SER GLU VAL ASP THR GLU ILE ASP TRP VAL ILE LYS SEQRES 28 A 493 LYS LYS LEU ILE ASP ARG PHE ILE GLN ARG GLY ASN LEU SEQRES 29 A 493 GLY LEU ASP ASP PRO LYS LEU ALA GLN VAL ASP LEU THR SEQRES 30 A 493 TYR HIS ASP ILE ARG PRO GLY ARG GLY LEU PHE SER VAL SEQRES 31 A 493 LEU GLN SER ARG GLY MET ILE LYS ARG TRP THR THR ASP SEQRES 32 A 493 GLU ALA ILE LEU ALA ALA VAL ASP THR ALA PRO ASP THR SEQRES 33 A 493 THR ARG ALA HIS LEU ARG GLY ARG ILE LEU LYS ALA ALA SEQRES 34 A 493 ASP THR LEU GLY VAL PRO VAL THR VAL ASP TRP MET ARG SEQRES 35 A 493 HIS LYS VAL ASN ARG PRO GLU PRO GLN SER VAL GLU LEU SEQRES 36 A 493 GLY ASP PRO PHE SER ALA VAL ASN SER GLU VAL ASP GLN SEQRES 37 A 493 LEU ILE GLU TYR MET THR VAL HIS ALA GLU SER TYR ARG SEQRES 38 A 493 SER LYS SER SER VAL GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 493 MET SER THR VAL GLU SER ALA LEU THR ARG ARG ILE MET SEQRES 2 B 493 GLY ILE GLU THR GLU TYR GLY LEU THR PHE VAL ASP GLY SEQRES 3 B 493 ASP SER LYS LYS LEU ARG PRO ASP GLU ILE ALA ARG ARG SEQRES 4 B 493 MET PHE ARG PRO ILE VAL GLU LYS TYR SER SER SER ASN SEQRES 5 B 493 ILE PHE ILE PRO ASN GLY SER ARG LEU TYR LEU ASP VAL SEQRES 6 B 493 GLY SER HIS PRO GLU TYR ALA THR ALA GLU CYS ASP ASN SEQRES 7 B 493 LEU THR GLN LEU ILE ASN PHE GLU LYS ALA GLY ASP VAL SEQRES 8 B 493 ILE ALA ASP ARG MET ALA VAL ASP ALA GLU GLU SER LEU SEQRES 9 B 493 ALA LYS GLU ASP ILE ALA GLY GLN VAL TYR LEU PHE LYS SEQRES 10 B 493 ASN ASN VAL ASP SER VAL GLY ASN SER TYR GLY CYS HIS SEQRES 11 B 493 GLU ASN TYR LEU VAL GLY ARG SER MET PRO LEU LYS ALA SEQRES 12 B 493 LEU GLY LYS ARG LEU MET PRO PHE LEU ILE THR ARG GLN SEQRES 13 B 493 LEU ILE CYS GLY ALA GLY ARG ILE HIS HIS PRO ASN PRO SEQRES 14 B 493 LEU ASP LYS GLY GLU SER PHE PRO LEU GLY TYR CYS ILE SEQRES 15 B 493 SER GLN ARG SER ASP HIS VAL TRP GLU GLY VAL SER SER SEQRES 16 B 493 ALA THR THR ARG SER ARG PRO ILE ILE ASN THR ARG ASP SEQRES 17 B 493 GLU PRO HIS ALA ASP SER HIS SER TYR ARG ARG LEU HIS SEQRES 18 B 493 VAL ILE VAL GLY ASP ALA ASN MET ALA GLU PRO SER ILE SEQRES 19 B 493 ALA LEU LYS VAL GLY SER THR LEU LEU VAL LEU GLU MET SEQRES 20 B 493 ILE GLU ALA ASP PHE GLY LEU PRO SER LEU GLU LEU ALA SEQRES 21 B 493 ASN ASP ILE ALA SER ILE ARG GLU ILE SER ARG ASP ALA SEQRES 22 B 493 THR GLY SER THR LEU LEU SER LEU LYS ASP GLY THR THR SEQRES 23 B 493 MET THR ALA LEU GLN ILE GLN GLN VAL VAL PHE GLU HIS SEQRES 24 B 493 ALA SER LYS TRP LEU GLU GLN ARG PRO GLU PRO GLU PHE SEQRES 25 B 493 SER GLY THR SER ASN THR GLU MET ALA ARG VAL LEU ASP SEQRES 26 B 493 LEU TRP GLY ARG MET LEU LYS ALA ILE GLU SER GLY ASP SEQRES 27 B 493 PHE SER GLU VAL ASP THR GLU ILE ASP TRP VAL ILE LYS SEQRES 28 B 493 LYS LYS LEU ILE ASP ARG PHE ILE GLN ARG GLY ASN LEU SEQRES 29 B 493 GLY LEU ASP ASP PRO LYS LEU ALA GLN VAL ASP LEU THR SEQRES 30 B 493 TYR HIS ASP ILE ARG PRO GLY ARG GLY LEU PHE SER VAL SEQRES 31 B 493 LEU GLN SER ARG GLY MET ILE LYS ARG TRP THR THR ASP SEQRES 32 B 493 GLU ALA ILE LEU ALA ALA VAL ASP THR ALA PRO ASP THR SEQRES 33 B 493 THR ARG ALA HIS LEU ARG GLY ARG ILE LEU LYS ALA ALA SEQRES 34 B 493 ASP THR LEU GLY VAL PRO VAL THR VAL ASP TRP MET ARG SEQRES 35 B 493 HIS LYS VAL ASN ARG PRO GLU PRO GLN SER VAL GLU LEU SEQRES 36 B 493 GLY ASP PRO PHE SER ALA VAL ASN SER GLU VAL ASP GLN SEQRES 37 B 493 LEU ILE GLU TYR MET THR VAL HIS ALA GLU SER TYR ARG SEQRES 38 B 493 SER LYS SER SER VAL GLU HIS HIS HIS HIS HIS HIS HET ADP A1478 76 HET MG A1479 1 HET ADP B1479 39 HET MG B1480 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *434(H2 O) HELIX 1 1 THR A 3 ALA A 7 5 5 HELIX 2 2 PRO A 33 SER A 49 1 17 HELIX 3 3 ASN A 78 GLU A 107 1 30 HELIX 4 4 LYS A 142 ARG A 147 1 6 HELIX 5 5 ARG A 147 GLY A 160 1 14 HELIX 6 6 ARG A 185 SER A 195 1 11 HELIX 7 7 ALA A 230 ASP A 251 1 22 HELIX 8 8 SER A 265 ARG A 271 1 7 HELIX 9 9 ALA A 289 ARG A 307 1 19 HELIX 10 10 SER A 316 GLY A 337 1 22 HELIX 11 11 ILE A 346 ASN A 363 1 18 HELIX 12 12 ASP A 368 TYR A 378 1 11 HELIX 13 13 GLY A 386 ARG A 394 1 9 HELIX 14 14 THR A 402 THR A 412 1 11 HELIX 15 15 ARG A 418 GLY A 433 1 16 HELIX 16 16 ASN A 463 ALA A 477 1 15 HELIX 17 17 THR B 3 ALA B 7 5 5 HELIX 18 18 ARG B 32 SER B 49 1 18 HELIX 19 19 ASN B 78 GLU B 107 1 30 HELIX 20 20 PRO B 140 GLY B 160 1 21 HELIX 21 21 ARG B 185 SER B 194 1 10 HELIX 22 22 ALA B 230 ALA B 250 1 21 HELIX 23 23 SER B 265 ASP B 272 1 8 HELIX 24 24 ALA B 289 ARG B 307 1 19 HELIX 25 25 SER B 316 GLY B 337 1 22 HELIX 26 26 ILE B 346 ASN B 363 1 18 HELIX 27 27 ASP B 368 TYR B 378 1 11 HELIX 28 28 GLY B 386 ARG B 394 1 9 HELIX 29 29 THR B 402 THR B 412 1 11 HELIX 30 30 ARG B 418 GLY B 433 1 16 HELIX 31 31 ASN B 463 HIS B 476 1 14 SHEET 1 BA 7 ASN B 52 PHE B 54 0 SHEET 2 BA 7 ARG B 60 TYR B 62 -1 O LEU B 61 N ILE B 53 SHEET 3 BA 7 GLU B 70 ALA B 72 -1 O GLU B 70 N TYR B 62 SHEET 4 BA 7 MET A 13 GLU A 18 -1 O THR A 17 N TYR B 71 SHEET 5 BA 7 CYS B 129 GLY B 136 -1 O HIS B 130 N GLU A 16 SHEET 6 BA 7 TYR B 217 VAL B 222 -1 O ARG B 218 N VAL B 135 SHEET 7 BA 7 ILE B 204 ASN B 205 -1 O ASN B 205 N HIS B 221 SHEET 1 AA 2 GLY A 20 VAL A 24 0 SHEET 2 AA 2 GLN B 112 PHE B 116 -1 O GLN B 112 N VAL A 24 SHEET 1 AB 7 ASN A 52 PHE A 54 0 SHEET 2 AB 7 ARG A 60 TYR A 62 -1 O LEU A 61 N ILE A 53 SHEET 3 AB 7 GLU A 70 ALA A 72 -1 O GLU A 70 N TYR A 62 SHEET 4 AB 7 MET B 13 GLU B 18 -1 O THR B 17 N TYR A 71 SHEET 5 AB 7 CYS A 129 GLY A 136 -1 O HIS A 130 N GLU B 16 SHEET 6 AB 7 TYR A 217 VAL A 222 -1 O ARG A 218 N VAL A 135 SHEET 7 AB 7 ILE A 204 ASN A 205 -1 O ASN A 205 N HIS A 221 SHEET 1 AC 2 GLN A 112 PHE A 116 0 SHEET 2 AC 2 GLY B 20 VAL B 24 -1 O GLY B 20 N PHE A 116 SHEET 1 AD 2 ARG A 163 HIS A 165 0 SHEET 2 AD 2 GLY A 179 CYS A 181 -1 O GLY A 179 N HIS A 165 SHEET 1 AE 2 LEU A 278 SER A 280 0 SHEET 2 AE 2 THR A 286 THR A 288 -1 O MET A 287 N LEU A 279 SHEET 1 AF 3 VAL A 436 VAL A 438 0 SHEET 2 AF 3 ARG A 442 VAL A 445 -1 O LYS A 444 N THR A 437 SHEET 3 AF 3 GLN A 451 GLU A 454 -1 O GLN A 451 N VAL A 445 SHEET 1 BB 2 ARG B 163 HIS B 165 0 SHEET 2 BB 2 GLY B 179 CYS B 181 -1 O GLY B 179 N HIS B 165 SHEET 1 BC 2 LEU B 278 SER B 280 0 SHEET 2 BC 2 THR B 286 THR B 288 -1 O MET B 287 N LEU B 279 SHEET 1 BD 3 THR B 437 VAL B 438 0 SHEET 2 BD 3 ARG B 442 VAL B 445 -1 O LYS B 444 N THR B 437 SHEET 3 BD 3 GLN B 451 GLU B 454 -1 O GLN B 451 N VAL B 445 LINK OE1 GLU A 16 MG MG B1480 1555 1555 2.52 LINK O1AAADP A1478 MG MG A1479 1555 1555 2.12 LINK O2BBADP A1478 MG MG A1479 1555 1555 2.54 LINK MG MG A1479 O HOH A2053 1555 1555 2.21 LINK MG MG A1479 O HOH A2063 1555 1555 2.49 LINK MG MG A1479 O HOH A2250 1555 1555 2.27 LINK MG MG A1479 O HOH A2251 1555 1555 2.29 LINK MG MG A1479 OE1 GLU B 16 1555 1555 2.32 LINK O HOH A2016 MG MG B1480 1555 1555 2.39 LINK O HOH A2017 MG MG B1480 1555 1555 2.78 LINK O HOH A2018 MG MG B1480 1555 1555 2.38 LINK O HOH A2235 MG MG B1480 1555 1555 2.73 LINK O1B ADP B1479 MG MG B1480 1555 1555 2.38 CISPEP 1 ARG A 447 PRO A 448 0 -8.25 CISPEP 2 ARG B 447 PRO B 448 0 -4.93 SITE 1 AC1 24 ARG A 60 THR A 73 GLU A 75 ASN A 132 SITE 2 AC1 24 LEU A 134 ASP A 208 PRO A 210 HIS A 211 SITE 3 AC1 24 ARG A 219 ARG A 418 TRP A 440 PRO A 458 SITE 4 AC1 24 MG A1479 HOH A2053 HOH A2250 HOH A2251 SITE 5 AC1 24 HOH A2252 ILE B 12 GLY B 14 ILE B 15 SITE 6 AC1 24 GLU B 16 LYS B 444 ASN B 446 PRO B 450 SITE 1 AC2 6 ADP A1478 HOH A2053 HOH A2063 HOH A2250 SITE 2 AC2 6 HOH A2251 GLU B 16 SITE 1 AC3 19 GLY A 14 ILE A 15 GLU A 16 HOH A2016 SITE 2 AC3 19 HOH A2235 HOH A2236 ARG B 60 THR B 73 SITE 3 AC3 19 ALA B 74 GLU B 75 ASN B 132 LEU B 134 SITE 4 AC3 19 PRO B 210 HIS B 211 ARG B 219 ARG B 418 SITE 5 AC3 19 TRP B 440 PRO B 458 MG B1480 SITE 1 AC4 6 GLU A 16 HOH A2016 HOH A2017 HOH A2018 SITE 2 AC4 6 HOH A2235 ADP B1479 CRYST1 62.100 118.810 163.020 90.00 90.00 90.00 P 21 21 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 0.016103 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006134 0.00000