HEADER HYDROLASE 08-JAN-20 6TUV TITLE CRYSTAL STRUCTURE OF MINDY1 IN COMPLEX WITH LYS48 LINKED DI-UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE MINDY-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME MINDY-1,PROTEIN FAM63A; COMPND 5 EC: 3.4.19.12; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: POLYUBIQUITIN-C; COMPND 9 CHAIN: H, D, L; COMPND 10 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: MINDY1, FAM63A, KIAA1390; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBC; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, CYSTEINE PROTEASE, ISOPEPTIDASE AND UBIQUITIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.A.ABDUL REHMAN,Y.KULATHU REVDAT 4 24-JAN-24 6TUV 1 REMARK REVDAT 3 03-NOV-21 6TUV 1 JRNL REVDAT 2 13-OCT-21 6TUV 1 JRNL REVDAT 1 27-JAN-21 6TUV 0 JRNL AUTH S.A.ABDUL REHMAN,L.A.ARMSTRONG,S.M.LANGE,Y.A.KRISTARIYANTO, JRNL AUTH 2 T.W.GRAWERT,A.KNEBEL,D.I.SVERGUN,Y.KULATHU JRNL TITL MECHANISM OF ACTIVATION AND REGULATION OF DEUBIQUITINASE JRNL TITL 2 ACTIVITY IN MINDY1 AND MINDY2. JRNL REF MOL.CELL V. 81 4176 2021 JRNL REFN ISSN 1097-2765 JRNL PMID 34529927 JRNL DOI 10.1016/J.MOLCEL.2021.08.024 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0257 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29517 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 + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1517 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2115 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3451 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.18000 REMARK 3 B22 (A**2) : 2.18000 REMARK 3 B33 (A**2) : -4.37000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.190 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3516 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3263 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4775 ; 1.608 ; 1.640 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7578 ; 1.263 ; 1.575 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 441 ; 7.319 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;35.473 ;24.099 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 598 ;17.096 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;16.779 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 483 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3867 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 660 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6TUV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 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) : 0.939274 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31102 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160 REMARK 200 RESOLUTION RANGE LOW (A) : 41.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.95500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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: 5JKN, 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, 200MM LISO4.H2O, 30% REMARK 280 PEG400, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 101.43350 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 50.71675 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 152.15025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 101.43350 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 152.15025 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 50.71675 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L 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 GLY A 96 REMARK 465 PRO A 97 REMARK 465 LEU A 98 REMARK 465 GLY A 99 REMARK 465 SER A 100 REMARK 465 PRO A 101 REMARK 465 GLU A 102 REMARK 465 PHE A 103 REMARK 465 PRO A 104 REMARK 465 GLY A 105 REMARK 465 ARG A 106 REMARK 465 LEU A 107 REMARK 465 LEU A 370 REMARK 465 GLY A 371 REMARK 465 LYS A 372 REMARK 465 GLY A 373 REMARK 465 PRO A 374 REMARK 465 GLY A 375 REMARK 465 ALA A 376 REMARK 465 GLU A 377 REMARK 465 GLY A 378 REMARK 465 GLY A 379 REMARK 465 SER A 380 REMARK 465 GLY A 381 REMARK 465 SER A 382 REMARK 465 PRO A 383 REMARK 465 GLU A 384 REMARK 465 ARG H 72 REMARK 465 LEU H 73 REMARK 465 ARG H 74 REMARK 465 GLY H 75 REMARK 465 GLY H 76 REMARK 465 MET L 1 REMARK 465 GLN L 2 REMARK 465 ILE L 3 REMARK 465 PHE L 4 REMARK 465 VAL L 5 REMARK 465 LYS L 6 REMARK 465 THR L 7 REMARK 465 LEU L 8 REMARK 465 THR L 9 REMARK 465 GLY L 10 REMARK 465 LYS L 11 REMARK 465 THR L 12 REMARK 465 ILE L 13 REMARK 465 THR L 14 REMARK 465 LEU L 15 REMARK 465 GLU L 16 REMARK 465 VAL L 17 REMARK 465 GLU L 18 REMARK 465 PRO L 19 REMARK 465 ASP L 32 REMARK 465 LYS L 33 REMARK 465 GLU L 34 REMARK 465 GLY L 35 REMARK 465 PHE L 45 REMARK 465 ALA L 46 REMARK 465 GLY L 47 REMARK 465 ASN L 60 REMARK 465 ILE L 61 REMARK 465 GLN L 62 REMARK 465 LYS L 63 REMARK 465 GLU L 64 REMARK 465 SER L 65 REMARK 465 THR L 66 REMARK 465 LEU L 67 REMARK 465 ARG L 74 REMARK 465 GLY L 75 REMARK 465 GLY L 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 GLU A 108 CG CD OE1 OE2 REMARK 470 MET A 109 CG SD CE REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 GLU A 181 CG CD OE1 OE2 REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 SER A 183 OG REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 GLN A 245 CG CD OE1 NE2 REMARK 470 LYS H 6 CE NZ REMARK 470 GLU H 24 CG CD OE1 OE2 REMARK 470 LEU H 71 CG CD1 CD2 REMARK 470 LYS D 11 CG CD CE NZ REMARK 470 GLU D 24 CG CD OE1 OE2 REMARK 470 LYS D 33 CG CD CE NZ REMARK 470 GLU D 34 CG CD OE1 OE2 REMARK 470 GLU D 51 CG CD OE1 OE2 REMARK 470 ASN D 60 CG OD1 ND2 REMARK 470 GLN D 62 CG CD OE1 NE2 REMARK 470 LYS D 63 CG CD CE NZ REMARK 470 GLU D 64 CG CD OE1 OE2 REMARK 470 SER D 65 OG REMARK 470 GLU L 24 CG CD OE1 OE2 REMARK 470 ILE L 36 CG1 CG2 CD1 REMARK 470 ASP L 39 CG OD1 OD2 REMARK 470 GLN L 40 CG CD OE1 NE2 REMARK 470 ILE L 44 CG1 CG2 CD1 REMARK 470 LYS L 48 CG CD CE NZ REMARK 470 GLN L 49 CG CD OE1 NE2 REMARK 470 ASP L 58 CG OD1 OD2 REMARK 470 HIS L 68 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 NZ LYS H 48 C GLY D 76 1.37 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 LEU A 186 -128.38 54.50 REMARK 500 SER A 246 70.30 -115.06 REMARK 500 PHE A 364 33.96 71.29 REMARK 500 ALA D 46 49.14 38.26 REMARK 500 GLU D 64 -2.25 73.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 401 DBREF 6TUV A 110 384 UNP Q8N5J2 MINY1_HUMAN 110 384 DBREF 6TUV H 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 6TUV D 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 6TUV L 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQADV 6TUV GLY A 96 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV PRO A 97 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV LEU A 98 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV GLY A 99 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV SER A 100 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV PRO A 101 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV GLU A 102 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV PHE A 103 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV PRO A 104 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV GLY A 105 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV ARG A 106 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV LEU A 107 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV GLU A 108 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV MET A 109 UNP Q8N5J2 EXPRESSION TAG SEQADV 6TUV ALA A 137 UNP Q8N5J2 CYS 137 ENGINEERED MUTATION SEQRES 1 A 289 GLY PRO LEU GLY SER PRO GLU PHE PRO GLY ARG LEU GLU SEQRES 2 A 289 MET GLU PRO ASP PHE TYR CYS VAL LYS TRP ILE PRO TRP SEQRES 3 A 289 LYS GLY GLU GLN THR PRO ILE ILE THR GLN SER THR ASN SEQRES 4 A 289 GLY PRO ALA PRO LEU LEU ALA ILE MET ASN ILE LEU PHE SEQRES 5 A 289 LEU GLN TRP LYS VAL LYS LEU PRO PRO GLN LYS GLU VAL SEQRES 6 A 289 ILE THR SER ASP GLU LEU MET ALA HIS LEU GLY ASN CYS SEQRES 7 A 289 LEU LEU SER ILE LYS PRO GLN GLU LYS SER GLU GLY LEU SEQRES 8 A 289 GLN LEU ASN PHE GLN GLN ASN VAL ASP ASP ALA MET THR SEQRES 9 A 289 VAL LEU PRO LYS LEU ALA THR GLY LEU ASP VAL ASN VAL SEQRES 10 A 289 ARG PHE THR GLY VAL SER ASP PHE GLU TYR THR PRO GLU SEQRES 11 A 289 CYS SER VAL PHE ASP LEU LEU GLY ILE PRO LEU TYR HIS SEQRES 12 A 289 GLY TRP LEU VAL ASP PRO GLN SER PRO GLU ALA VAL ARG SEQRES 13 A 289 ALA VAL GLY LYS LEU SER TYR ASN GLN LEU VAL GLU ARG SEQRES 14 A 289 ILE ILE THR CYS LYS HIS SER SER ASP THR ASN LEU VAL SEQRES 15 A 289 THR GLU GLY LEU ILE ALA GLU GLN PHE LEU GLU THR THR SEQRES 16 A 289 ALA ALA GLN LEU THR TYR HIS GLY LEU CYS GLU LEU THR SEQRES 17 A 289 ALA ALA ALA LYS GLU GLY GLU LEU SER VAL PHE PHE ARG SEQRES 18 A 289 ASN ASN HIS PHE SER THR MET THR LYS HIS LYS SER HIS SEQRES 19 A 289 LEU TYR LEU LEU VAL THR ASP GLN GLY PHE LEU GLN GLU SEQRES 20 A 289 GLU GLN VAL VAL TRP GLU SER LEU HIS ASN VAL ASP GLY SEQRES 21 A 289 ASP SER CYS PHE CYS ASP SER ASP PHE HIS LEU SER HIS SEQRES 22 A 289 SER LEU GLY LYS GLY PRO GLY ALA GLU GLY GLY SER GLY SEQRES 23 A 289 SER PRO GLU SEQRES 1 H 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 H 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 H 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 H 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 H 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 H 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 D 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 L 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 L 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 L 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 L 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 L 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 L 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET SO4 A 401 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *104(H2 O) HELIX 1 AA1 PRO A 136 GLN A 149 1 14 HELIX 2 AA2 SER A 163 SER A 176 1 14 HELIX 3 AA3 GLN A 187 LEU A 201 1 15 HELIX 4 AA4 PRO A 202 THR A 206 5 5 HELIX 5 AA5 THR A 223 LEU A 232 1 10 HELIX 6 AA6 SER A 246 GLY A 254 1 9 HELIX 7 AA7 SER A 257 HIS A 270 1 14 HELIX 8 AA8 ASP A 273 THR A 290 1 18 HELIX 9 AA9 THR A 295 ALA A 306 1 12 HELIX 10 AB1 ASP A 336 LEU A 340 5 5 HELIX 11 AB2 THR H 22 GLY H 35 1 14 HELIX 12 AB3 PRO H 37 GLN H 41 5 5 HELIX 13 AB4 LEU H 56 ASN H 60 5 5 HELIX 14 AB5 THR D 22 GLU D 34 1 13 HELIX 15 AB6 PRO D 37 ASP D 39 5 3 HELIX 16 AB7 LEU D 56 ASN D 60 5 5 HELIX 17 AB8 THR L 22 GLN L 31 1 10 HELIX 18 AB9 PRO L 37 ASP L 39 5 3 HELIX 19 AC1 THR L 55 TYR L 59 5 5 SHEET 1 AA1 3 GLU A 124 ILE A 129 0 SHEET 2 AA1 3 PHE A 113 TRP A 121 -1 N LYS A 117 O ILE A 128 SHEET 3 AA1 3 VAL A 160 THR A 162 -1 O ILE A 161 N TYR A 114 SHEET 1 AA2 2 LEU A 208 VAL A 210 0 SHEET 2 AA2 2 LEU D 73 GLY D 75 -1 O GLY D 75 N LEU A 208 SHEET 1 AA3 6 LEU A 236 TYR A 237 0 SHEET 2 AA3 6 LEU A 311 PHE A 315 1 O VAL A 313 N TYR A 237 SHEET 3 AA3 6 PHE A 320 HIS A 326 -1 O MET A 323 N SER A 312 SHEET 4 AA3 6 HIS A 329 LEU A 333 -1 O TYR A 331 N THR A 324 SHEET 5 AA3 6 TRP A 347 LEU A 350 -1 O GLU A 348 N LEU A 332 SHEET 6 AA3 6 PHE A 359 CYS A 360 -1 O CYS A 360 N TRP A 347 SHEET 1 AA4 5 THR H 12 GLU H 16 0 SHEET 2 AA4 5 GLN H 2 LYS H 6 -1 N VAL H 5 O ILE H 13 SHEET 3 AA4 5 THR H 66 VAL H 70 1 O LEU H 67 N PHE H 4 SHEET 4 AA4 5 ARG H 42 PHE H 45 -1 N ILE H 44 O HIS H 68 SHEET 5 AA4 5 LYS H 48 LEU H 50 -1 O LEU H 50 N LEU H 43 SHEET 1 AA5 5 THR D 12 GLU D 16 0 SHEET 2 AA5 5 GLN D 2 LYS D 6 -1 N ILE D 3 O LEU D 15 SHEET 3 AA5 5 THR D 66 LEU D 71 1 O LEU D 67 N PHE D 4 SHEET 4 AA5 5 GLN D 41 PHE D 45 -1 N ILE D 44 O HIS D 68 SHEET 5 AA5 5 LYS D 48 GLN D 49 -1 O LYS D 48 N PHE D 45 SHEET 1 AA6 2 GLN L 41 LEU L 43 0 SHEET 2 AA6 2 LEU L 69 LEU L 71 -1 O VAL L 70 N ARG L 42 SSBOND 1 CYS A 358 CYS A 358 1555 5655 2.74 SITE 1 AC1 4 ALA A 306 LYS A 307 GLU A 308 LYS A 325 CRYST1 73.862 73.862 202.867 90.00 90.00 90.00 P 41 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 0.013539 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004929 0.00000