HEADER HYDROLASE 17-JUL-17 5OHP TITLE CRYSTAL STRUCTURE OF USP30 (C77A) IN COMPLEX WITH LYS6-LINKED TITLE 2 DIUBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 30; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 64-178,UNP RESIDUES 217-357,UNP RESIDUES 432- COMPND 5 502; COMPND 6 SYNONYM: DEUBIQUITINATING ENZYME 30,UBIQUITIN THIOESTERASE 30, COMPND 7 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 30,UB-SPECIFIC PROTEASE 30; COMPND 8 EC: 3.4.19.12,3.4.19.12,3.4.19.12; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: POLYUBIQUITIN-B; COMPND 13 CHAIN: B, C; COMPND 14 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: USP30; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 PLACI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: POPIN-3C-K; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MG-31-28; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UBB; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 PLACI; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PET17B KEYWDS DUB, UBIQUITIN, USP, K6, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GERSCH,D.KOMANDER REVDAT 6 17-JAN-24 5OHP 1 REMARK REVDAT 5 10-JUL-19 5OHP 1 REMARK REVDAT 4 08-MAY-19 5OHP 1 REMARK LINK REVDAT 3 15-NOV-17 5OHP 1 JRNL REVDAT 2 04-OCT-17 5OHP 1 JRNL REVDAT 1 20-SEP-17 5OHP 0 JRNL AUTH M.GERSCH,C.GLADKOVA,A.F.SCHUBERT,M.A.MICHEL,S.MASLEN, JRNL AUTH 2 D.KOMANDER JRNL TITL MECHANISM AND REGULATION OF THE LYS6-SELECTIVE JRNL TITL 2 DEUBIQUITINASE USP30. JRNL REF NAT. STRUCT. MOL. BIOL. V. 24 920 2017 JRNL REFN ESSN 1545-9985 JRNL PMID 28945249 JRNL DOI 10.1038/NSMB.3475 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11RC1_2513) 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 14379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 729 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 82.1120 - 4.7881 0.97 2843 146 0.1998 0.2138 REMARK 3 2 4.7881 - 3.8005 1.00 2754 148 0.1778 0.2315 REMARK 3 3 3.8005 - 3.3200 1.00 2703 154 0.2229 0.2471 REMARK 3 4 3.3200 - 3.0165 1.00 2664 153 0.2621 0.3098 REMARK 3 5 3.0165 - 2.8003 1.00 2686 128 0.3088 0.3474 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.70 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 : 0.005 3767 REMARK 3 ANGLE : 0.695 5102 REMARK 3 CHIRALITY : 0.223 583 REMARK 3 PLANARITY : 0.004 651 REMARK 3 DIHEDRAL : 25.017 1365 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 5OHP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005835. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96860 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14395 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 82.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.17020 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.99770 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.830 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: 5OHK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.73 M SODIUM CITRATE, 0.1 M HEPES PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 92.56133 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 46.28067 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 69.42100 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 23.14033 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 115.70167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 92.56133 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 46.28067 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 23.14033 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 69.42100 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 115.70167 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 912 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 926 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 109 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 111 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 62 REMARK 465 PRO A 63 REMARK 465 ARG A 105 REMARK 465 ASP A 106 REMARK 465 GLN A 107 REMARK 465 LYS A 108 REMARK 465 GLU A 109 REMARK 465 PRO A 110 REMARK 465 PRO A 111 REMARK 465 SER A 112 REMARK 465 GLU A 291 REMARK 465 ALA A 292 REMARK 465 LYS A 293 REMARK 465 GLY A 294 REMARK 465 THR A 295 REMARK 465 LEU A 296 REMARK 465 ASN A 297 REMARK 465 GLY A 298 REMARK 465 GLU A 299 REMARK 465 LYS A 300 REMARK 465 VAL A 301 REMARK 465 GLY C 75 REMARK 465 GLY C 76 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 GLN A 130 CG CD OE1 NE2 REMARK 470 ASP A 134 CG OD1 OD2 REMARK 470 LYS A 219 CG CD CE NZ REMARK 470 THR A 288 OG1 CG2 REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 GLU A 302 CG CD OE1 OE2 REMARK 470 ASN A 359 CG OD1 ND2 REMARK 470 SER A 432 OG REMARK 470 ARG A 464 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 465 CG OD1 ND2 REMARK 470 LYS A 483 CG CD CE NZ REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 LYS B 63 CD CE NZ REMARK 470 GLU C 16 CG CD OE1 OE2 REMARK 470 GLU C 24 CG CD OE1 OE2 REMARK 470 ASP C 32 CG OD1 OD2 REMARK 470 ARG C 74 CG CD NE CZ NH1 NH2 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 C GLY B 76 NZ LYS C 6 1.27 REMARK 500 OE1 GLN A 160 O HOH A 901 1.90 REMARK 500 O GLY B 76 NZ LYS C 6 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 NE2 GLN A 487 NE2 GLN A 487 12564 1.43 REMARK 500 CD2 LEU C 8 CD2 LEU C 8 7554 1.62 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 GLN A 114 73.63 -118.85 REMARK 500 GLN A 153 87.73 -68.06 REMARK 500 HIS A 303 80.42 53.76 REMARK 500 THR A 306 -166.94 -105.23 REMARK 500 ASP A 447 -150.40 -90.46 REMARK 500 ASP A 478 -106.64 53.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 931 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A 932 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH C 110 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH C 111 DISTANCE = 9.55 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 800 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 CYS A 237 SG 98.0 REMARK 620 3 CYS A 284 SG 118.7 108.9 REMARK 620 4 CYS A 287 SG 110.2 115.3 106.1 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 800 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OHK RELATED DB: PDB DBREF 5OHP A 64 178 UNP Q70CQ3 UBP30_HUMAN 64 178 DBREF 5OHP A 217 357 UNP Q70CQ3 UBP30_HUMAN 217 357 DBREF 5OHP A 432 502 UNP Q70CQ3 UBP30_HUMAN 432 502 DBREF 5OHP B 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 5OHP C 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 5OHP GLY A 62 UNP Q70CQ3 EXPRESSION TAG SEQADV 5OHP PRO A 63 UNP Q70CQ3 EXPRESSION TAG SEQADV 5OHP ALA A 77 UNP Q70CQ3 CYS 77 ENGINEERED MUTATION SEQADV 5OHP GLY A 179 UNP Q70CQ3 LINKER SEQADV 5OHP SER A 180 UNP Q70CQ3 LINKER SEQADV 5OHP GLY A 181 UNP Q70CQ3 LINKER SEQADV 5OHP SER A 182 UNP Q70CQ3 LINKER SEQADV 5OHP ASP A 348 UNP Q70CQ3 PHE 348 ENGINEERED MUTATION SEQADV 5OHP SER A 350 UNP Q70CQ3 MET 350 ENGINEERED MUTATION SEQADV 5OHP GLU A 353 UNP Q70CQ3 ILE 353 ENGINEERED MUTATION SEQADV 5OHP SER A 358 UNP Q70CQ3 LINKER SEQADV 5OHP ASN A 359 UNP Q70CQ3 LINKER SEQADV 5OHP ALA A 360 UNP Q70CQ3 LINKER SEQRES 1 A 336 GLY PRO LYS GLY LEU VAL PRO GLY LEU VAL ASN LEU GLY SEQRES 2 A 336 ASN THR ALA PHE MET ASN SER LEU LEU GLN GLY LEU SER SEQRES 3 A 336 ALA CYS PRO ALA PHE ILE ARG TRP LEU GLU GLU PHE THR SEQRES 4 A 336 SER GLN TYR SER ARG ASP GLN LYS GLU PRO PRO SER HIS SEQRES 5 A 336 GLN TYR LEU SER LEU THR LEU LEU HIS LEU LEU LYS ALA SEQRES 6 A 336 LEU SER CYS GLN GLU VAL THR ASP ASP GLU VAL LEU ASP SEQRES 7 A 336 ALA SER CYS LEU LEU ASP VAL LEU ARG MET TYR ARG TRP SEQRES 8 A 336 GLN ILE SER SER PHE GLU GLU GLN ASP ALA HIS GLU LEU SEQRES 9 A 336 PHE HIS VAL ILE THR SER SER LEU GLU ASP GLU ARG ASP SEQRES 10 A 336 GLY SER GLY SER HIS TRP LYS SER GLN HIS PRO PHE HIS SEQRES 11 A 336 GLY ARG LEU THR SER ASN MET VAL CYS LYS HIS CYS GLU SEQRES 12 A 336 HIS GLN SER PRO VAL ARG PHE ASP THR PHE ASP SER LEU SEQRES 13 A 336 SER LEU SER ILE PRO ALA ALA THR TRP GLY HIS PRO LEU SEQRES 14 A 336 THR LEU ASP HIS CYS LEU HIS HIS PHE ILE SER SER GLU SEQRES 15 A 336 SER VAL ARG ASP VAL VAL CYS ASP ASN CYS THR LYS ILE SEQRES 16 A 336 GLU ALA LYS GLY THR LEU ASN GLY GLU LYS VAL GLU HIS SEQRES 17 A 336 GLN ARG THR THR PHE VAL LYS GLN LEU LYS LEU GLY LYS SEQRES 18 A 336 LEU PRO GLN CYS LEU CYS ILE HIS LEU GLN ARG LEU SER SEQRES 19 A 336 TRP SER SER HIS GLY THR PRO LEU LYS ARG HIS GLU HIS SEQRES 20 A 336 VAL GLN PHE ASN GLU ASP LEU SER MET ASP GLU TYR LYS SEQRES 21 A 336 TYR HIS SER ASN ALA SER THR TYR LEU PHE ARG LEU MET SEQRES 22 A 336 ALA VAL VAL VAL HIS HIS GLY ASP MET HIS SER GLY HIS SEQRES 23 A 336 PHE VAL THR TYR ARG ARG SER PRO PRO SER ALA ARG ASN SEQRES 24 A 336 PRO LEU SER THR SER ASN GLN TRP LEU TRP VAL SER ASP SEQRES 25 A 336 ASP THR VAL ARG LYS ALA SER LEU GLN GLU VAL LEU SER SEQRES 26 A 336 SER SER ALA TYR LEU LEU PHE TYR GLU ARG VAL SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET ZN A 800 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *52(H2 O) HELIX 1 AA1 THR A 76 ALA A 88 1 13 HELIX 2 AA2 CYS A 89 SER A 101 1 13 HELIX 3 AA3 GLN A 102 SER A 104 5 3 HELIX 4 AA4 TYR A 115 CYS A 129 1 15 HELIX 5 AA5 ALA A 140 ARG A 148 1 9 HELIX 6 AA6 ASP A 161 GLY A 179 1 19 HELIX 7 AA7 LEU A 266 SER A 275 1 10 HELIX 8 AA8 CYS A 284 LYS A 289 1 6 HELIX 9 AA9 ASP A 352 LYS A 355 5 4 HELIX 10 AB1 SER A 485 SER A 491 1 7 HELIX 11 AB2 THR B 22 GLY B 35 1 14 HELIX 12 AB3 PRO B 37 GLN B 41 5 5 HELIX 13 AB4 THR C 22 GLY C 35 1 14 HELIX 14 AB5 PRO C 37 ASP C 39 5 3 HELIX 15 AB6 THR C 55 ASN C 60 5 6 SHEET 1 AA1 2 GLY A 69 LEU A 70 0 SHEET 2 AA1 2 VAL A 137 LEU A 138 1 O LEU A 138 N GLY A 69 SHEET 1 AA2 4 ARG A 244 PHE A 248 0 SHEET 2 AA2 4 GLY A 226 CYS A 234 -1 N LEU A 228 O ASP A 246 SHEET 3 AA2 4 ARG A 305 LYS A 316 -1 O LYS A 313 N THR A 229 SHEET 4 AA2 4 SER A 276 VAL A 283 -1 N GLU A 277 O LYS A 310 SHEET 1 AA3 5 LEU A 251 SER A 254 0 SHEET 2 AA3 5 CYS A 320 GLN A 326 1 O HIS A 324 N LEU A 251 SHEET 3 AA3 5 ALA A 494 ARG A 501 -1 O TYR A 499 N LEU A 321 SHEET 4 AA3 5 LEU A 435 GLY A 446 -1 N VAL A 442 O LEU A 496 SHEET 5 AA3 5 ASP A 348 SER A 350 -1 N LEU A 349 O PHE A 436 SHEET 1 AA4 7 LEU A 251 SER A 254 0 SHEET 2 AA4 7 CYS A 320 GLN A 326 1 O HIS A 324 N LEU A 251 SHEET 3 AA4 7 ALA A 494 ARG A 501 -1 O TYR A 499 N LEU A 321 SHEET 4 AA4 7 LEU A 435 GLY A 446 -1 N VAL A 442 O LEU A 496 SHEET 5 AA4 7 GLY A 451 ARG A 458 -1 O TYR A 456 N VAL A 441 SHEET 6 AA4 7 TRP A 473 SER A 477 -1 O LEU A 474 N ARG A 457 SHEET 7 AA4 7 THR A 480 ALA A 484 -1 O ARG A 482 N TRP A 475 SHEET 1 AA5 2 LEU A 264 THR A 265 0 SHEET 2 AA5 2 VAL A 343 GLN A 344 1 O GLN A 344 N LEU A 264 SHEET 1 AA6 2 LEU A 328 TRP A 330 0 SHEET 2 AA6 2 PRO A 336 LYS A 338 -1 O LEU A 337 N SER A 329 SHEET 1 AA7 5 THR B 12 GLU B 16 0 SHEET 2 AA7 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 AA7 5 THR B 66 VAL B 70 1 O LEU B 67 N PHE B 4 SHEET 4 AA7 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA7 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA8 5 THR C 12 GLU C 16 0 SHEET 2 AA8 5 GLN C 2 THR C 7 -1 N ILE C 3 O LEU C 15 SHEET 3 AA8 5 THR C 66 LEU C 71 1 O LEU C 67 N LYS C 6 SHEET 4 AA8 5 GLN C 41 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 AA8 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK SG CYS A 234 ZN ZN A 800 1555 1555 2.36 LINK SG CYS A 237 ZN ZN A 800 1555 1555 2.35 LINK SG CYS A 284 ZN ZN A 800 1555 1555 2.34 LINK SG CYS A 287 ZN ZN A 800 1555 1555 2.35 SITE 1 AC1 4 CYS A 234 CYS A 237 CYS A 284 CYS A 287 CRYST1 117.504 117.504 138.842 90.00 90.00 120.00 P 65 2 2 24 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 0.008510 0.004913 0.000000 0.00000 SCALE2 0.000000 0.009827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007202 0.00000