HEADER HYDROLASE 22-JUL-15 5CRA TITLE STRUCTURE OF THE SDEA DUB DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SDEA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DUB DOMAIN (RESIDUES 6-198); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: POLYUBIQUITIN-B; COMPND 8 CHAIN: D, C; COMPND 9 FRAGMENT: UNP RESIDUES 1-75; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA; SOURCE 3 ORGANISM_TAXID: 446; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: UBB; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEUBIQUITINASE, LEGIONELLA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SHEEDLO,J.QIU,Z.Q.LUO,C.DAS REVDAT 5 15-NOV-23 5CRA 1 LINK ATOM REVDAT 4 04-DEC-19 5CRA 1 JRNL REMARK REVDAT 3 16-DEC-15 5CRA 1 JRNL REVDAT 2 09-DEC-15 5CRA 1 JRNL REVDAT 1 25-NOV-15 5CRA 0 JRNL AUTH M.J.SHEEDLO,J.QIU,Y.TAN,L.N.PAUL,Z.Q.LUO,C.DAS JRNL TITL STRUCTURAL BASIS OF SUBSTRATE RECOGNITION BY A BACTERIAL JRNL TITL 2 DEUBIQUITINASE IMPORTANT FOR DYNAMICS OF PHAGOSOME JRNL TITL 3 UBIQUITINATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 15090 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 26598703 JRNL DOI 10.1073/PNAS.1514568112 REMARK 2 REMARK 2 RESOLUTION. 2.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 843 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) : 2.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1123 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3766 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.02000 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): 3.941 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.316 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.221 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.303 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3894 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3694 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5290 ; 1.658 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8486 ; 1.054 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 490 ; 6.395 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;39.770 ;24.824 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 634 ;17.509 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;19.079 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 595 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4440 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 872 ; 0.002 ; 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): 1976 ; 2.484 ; 3.514 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1973 ; 2.484 ; 3.515 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2458 ; 3.802 ; 5.267 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2459 ; 3.801 ; 5.266 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1918 ; 3.348 ; 3.963 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1883 ; 3.311 ; 3.950 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2773 ; 5.329 ; 5.768 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4147 ; 6.935 ;27.956 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4145 ; 6.934 ;27.953 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 173 B 2 173 9852 0.03 0.05 REMARK 3 2 D 1 75 C 1 75 4855 0.01 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 REMARK 4 REMARK 4 5CRA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211653. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18407 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS:HCL, 3.0 M SODIUM CHLORIDE, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 80.47800 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 40.23900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 174 REMARK 465 PHE A 175 REMARK 465 PRO A 176 REMARK 465 GLU A 177 REMARK 465 GLY A 178 REMARK 465 ASP A 179 REMARK 465 PRO A 180 REMARK 465 GLN A 181 REMARK 465 LEU A 182 REMARK 465 ASP A 183 REMARK 465 GLY A 184 REMARK 465 LYS A 185 REMARK 465 ALA A 186 REMARK 465 LEU A 187 REMARK 465 ARG A 188 REMARK 465 GLU A 189 REMARK 465 ASN A 190 REMARK 465 THR A 191 REMARK 465 GLU A 192 REMARK 465 LYS A 193 REMARK 465 MET B 1 REMARK 465 GLU B 174 REMARK 465 PHE B 175 REMARK 465 PRO B 176 REMARK 465 GLU B 177 REMARK 465 GLY B 178 REMARK 465 ASP B 179 REMARK 465 PRO B 180 REMARK 465 GLN B 181 REMARK 465 LEU B 182 REMARK 465 ASP B 183 REMARK 465 GLY B 184 REMARK 465 LYS B 185 REMARK 465 ALA B 186 REMARK 465 LEU B 187 REMARK 465 ARG B 188 REMARK 465 GLU B 189 REMARK 465 ASN B 190 REMARK 465 THR B 191 REMARK 465 GLU B 192 REMARK 465 LYS B 193 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 PRO A 2 CG CD REMARK 470 MET A 100 CG SD CE REMARK 470 ARG A 169 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 6 CG CD CE NZ REMARK 470 LYS D 48 CG CD CE NZ REMARK 470 PRO B 2 CG CD REMARK 470 MET B 100 CG SD CE REMARK 470 ARG B 169 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 6 CG CD CE NZ REMARK 470 LYS C 48 CG CD CE NZ 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 PRO A 2 N - CA - CB ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG D 42 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 PRO B 2 N - CA - CB ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG C 42 NE - CZ - NH1 ANGL. DEV. = 4.7 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 LYS A 3 -53.57 -26.76 REMARK 500 SER A 124 -73.69 -119.60 REMARK 500 ASP A 159 31.37 72.94 REMARK 500 ASP D 39 -48.10 -23.20 REMARK 500 LYS B 3 -52.80 -27.28 REMARK 500 SER B 124 -73.45 -120.69 REMARK 500 ASP B 159 32.61 72.44 REMARK 500 ASP C 39 -48.05 -22.87 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GVE D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GVE C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CRB RELATED DB: PDB REMARK 900 RELATED ID: 5CRC RELATED DB: PDB DBREF 5CRA A 1 193 UNP Q6RCR0 Q6RCR0_LEGPN 6 198 DBREF 5CRA D 1 75 UNP P0CG47 UBB_HUMAN 1 75 DBREF 5CRA B 1 193 UNP Q6RCR0 Q6RCR0_LEGPN 6 198 DBREF 5CRA C 1 75 UNP P0CG47 UBB_HUMAN 1 75 SEQRES 1 A 193 MET PRO LYS TYR VAL GLU GLY VAL GLU LEU THR GLN GLU SEQRES 2 A 193 GLY MET HIS ALA ILE PHE ALA ARG MET GLY TYR GLY ASP SEQRES 3 A 193 ILE THR SER GLY SER ILE TYR ASN GLY VAL PRO THR ILE SEQRES 4 A 193 ASP THR GLY ALA LEU ASN ARG GLN GLY PHE MET PRO VAL SEQRES 5 A 193 LEU THR GLY VAL GLY PRO HIS ARG ASP SER GLY HIS TRP SEQRES 6 A 193 ILE MET LEU ILE LYS GLY PRO GLY ASN GLN TYR TYR LEU SEQRES 7 A 193 PHE ASP PRO LEU GLY LYS THR SER GLY GLU GLY TYR GLN SEQRES 8 A 193 ASN ILE LEU ALA ALA GLN LEU PRO MET GLY SER THR LEU SEQRES 9 A 193 SER VAL ILE PRO ASN GLY SER GLY LEU ASN MET GLY LEU SEQRES 10 A 193 CYS GLY TYR TRP VAL ALA SER ALA GLY LEU ARG ALA HIS SEQRES 11 A 193 GLN ALA LEU ASN GLN HIS ASN PRO PRO THR LEU LEU ASN SEQRES 12 A 193 VAL GLY GLN THR ILE THR ASN GLU MET ARG ASN GLU LEU SEQRES 13 A 193 ASP HIS ASP GLY TYR ARG LYS ILE THR GLY TRP LEU ARG SEQRES 14 A 193 ALA VAL ALA ASP GLU PHE PRO GLU GLY ASP PRO GLN LEU SEQRES 15 A 193 ASP GLY LYS ALA LEU ARG GLU ASN THR GLU LYS SEQRES 1 D 75 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 75 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 75 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 75 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 D 75 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 75 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 1 B 193 MET PRO LYS TYR VAL GLU GLY VAL GLU LEU THR GLN GLU SEQRES 2 B 193 GLY MET HIS ALA ILE PHE ALA ARG MET GLY TYR GLY ASP SEQRES 3 B 193 ILE THR SER GLY SER ILE TYR ASN GLY VAL PRO THR ILE SEQRES 4 B 193 ASP THR GLY ALA LEU ASN ARG GLN GLY PHE MET PRO VAL SEQRES 5 B 193 LEU THR GLY VAL GLY PRO HIS ARG ASP SER GLY HIS TRP SEQRES 6 B 193 ILE MET LEU ILE LYS GLY PRO GLY ASN GLN TYR TYR LEU SEQRES 7 B 193 PHE ASP PRO LEU GLY LYS THR SER GLY GLU GLY TYR GLN SEQRES 8 B 193 ASN ILE LEU ALA ALA GLN LEU PRO MET GLY SER THR LEU SEQRES 9 B 193 SER VAL ILE PRO ASN GLY SER GLY LEU ASN MET GLY LEU SEQRES 10 B 193 CYS GLY TYR TRP VAL ALA SER ALA GLY LEU ARG ALA HIS SEQRES 11 B 193 GLN ALA LEU ASN GLN HIS ASN PRO PRO THR LEU LEU ASN SEQRES 12 B 193 VAL GLY GLN THR ILE THR ASN GLU MET ARG ASN GLU LEU SEQRES 13 B 193 ASP HIS ASP GLY TYR ARG LYS ILE THR GLY TRP LEU ARG SEQRES 14 B 193 ALA VAL ALA ASP GLU PHE PRO GLU GLY ASP PRO GLN LEU SEQRES 15 B 193 ASP GLY LYS ALA LEU ARG GLU ASN THR GLU LYS SEQRES 1 C 75 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 75 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 75 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 75 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 75 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 75 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET SO4 A 205 5 HET SO4 A 206 5 HET GVE D 101 8 HET SO4 B 201 5 HET SO4 B 202 5 HET SO4 B 203 5 HET GVE C 101 8 HETNAM SO4 SULFATE ION HETNAM GVE METHYL 4-AMINOBUTANOATE FORMUL 5 SO4 9(O4 S 2-) FORMUL 11 GVE 2(C5 H11 N O2) FORMUL 16 HOH *32(H2 O) HELIX 1 AA1 GLN A 12 MET A 22 1 11 HELIX 2 AA2 ASP A 40 GLY A 48 1 9 HELIX 3 AA3 GLY A 83 GLY A 89 1 7 HELIX 4 AA4 TYR A 90 ALA A 96 1 7 HELIX 5 AA5 LEU A 117 SER A 124 1 8 HELIX 6 AA6 SER A 124 ASN A 134 1 11 HELIX 7 AA7 THR A 140 ASP A 157 1 18 HELIX 8 AA8 ASP A 159 ALA A 172 1 14 HELIX 9 AA9 THR D 22 GLY D 35 1 14 HELIX 10 AB1 PRO D 37 ASP D 39 5 3 HELIX 11 AB2 LEU D 56 ASN D 60 5 5 HELIX 12 AB3 GLN B 12 MET B 22 1 11 HELIX 13 AB4 ASP B 40 GLY B 48 1 9 HELIX 14 AB5 GLY B 83 GLY B 89 1 7 HELIX 15 AB6 TYR B 90 ALA B 96 1 7 HELIX 16 AB7 LEU B 117 SER B 124 1 8 HELIX 17 AB8 SER B 124 ASN B 134 1 11 HELIX 18 AB9 THR B 140 ASP B 157 1 18 HELIX 19 AC1 ASP B 159 ALA B 172 1 14 HELIX 20 AC2 THR C 22 GLY C 35 1 14 HELIX 21 AC3 PRO C 37 ASP C 39 5 3 HELIX 22 AC4 LEU C 56 ASN C 60 5 5 SHEET 1 AA1 3 VAL A 5 GLU A 6 0 SHEET 2 AA1 3 GLU A 9 THR A 11 -1 O GLU A 9 N GLU A 6 SHEET 3 AA1 3 ARG D 74 GLY D 75 -1 O GLY D 75 N LEU A 10 SHEET 1 AA2 6 VAL A 36 THR A 38 0 SHEET 2 AA2 6 GLY A 30 TYR A 33 -1 N SER A 31 O THR A 38 SHEET 3 AA2 6 PHE A 49 VAL A 56 1 O LEU A 53 N GLY A 30 SHEET 4 AA2 6 HIS A 64 LYS A 70 -1 O ILE A 66 N VAL A 52 SHEET 5 AA2 6 GLN A 75 PHE A 79 -1 O TYR A 77 N ILE A 69 SHEET 6 AA2 6 THR A 103 VAL A 106 1 O SER A 105 N LEU A 78 SHEET 1 AA3 5 THR D 12 GLU D 16 0 SHEET 2 AA3 5 GLN D 2 THR D 7 -1 N VAL D 5 O ILE D 13 SHEET 3 AA3 5 THR D 66 LEU D 71 1 O LEU D 69 N LYS D 6 SHEET 4 AA3 5 GLN D 41 PHE D 45 -1 N ARG D 42 O VAL D 70 SHEET 5 AA3 5 LYS D 48 GLN D 49 -1 O LYS D 48 N PHE D 45 SHEET 1 AA4 3 VAL B 5 GLU B 6 0 SHEET 2 AA4 3 GLU B 9 THR B 11 -1 O GLU B 9 N GLU B 6 SHEET 3 AA4 3 ARG C 74 GLY C 75 -1 O GLY C 75 N LEU B 10 SHEET 1 AA5 6 VAL B 36 THR B 38 0 SHEET 2 AA5 6 GLY B 30 TYR B 33 -1 N SER B 31 O THR B 38 SHEET 3 AA5 6 PHE B 49 VAL B 56 1 O LEU B 53 N GLY B 30 SHEET 4 AA5 6 HIS B 64 LYS B 70 -1 O ILE B 66 N VAL B 52 SHEET 5 AA5 6 GLN B 75 PHE B 79 -1 O TYR B 77 N ILE B 69 SHEET 6 AA5 6 THR B 103 VAL B 106 1 O SER B 105 N LEU B 78 SHEET 1 AA6 5 THR C 12 GLU C 16 0 SHEET 2 AA6 5 GLN C 2 THR C 7 -1 N VAL C 5 O ILE C 13 SHEET 3 AA6 5 THR C 66 LEU C 71 1 O LEU C 69 N LYS C 6 SHEET 4 AA6 5 GLN C 41 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 AA6 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK SG CYS A 118 CB GVE D 101 1555 1555 1.84 LINK C GLY D 75 N GVE D 101 1555 1555 1.27 LINK SG CYS B 118 CB GVE C 101 1555 1555 1.80 LINK C GLY C 75 N GVE C 101 1555 1555 1.27 SITE 1 AC1 5 PRO A 58 HIS A 59 ARG A 60 ASP B 157 SITE 2 AC1 5 HIS B 158 SITE 1 AC2 6 ARG A 60 TYR A 90 HOH A 306 ASP B 157 SITE 2 AC2 6 HIS B 158 ASP B 159 SITE 1 AC3 5 ASP A 157 HIS A 158 ASP A 159 ARG B 60 SITE 2 AC3 5 TYR B 90 SITE 1 AC4 5 LEU A 82 LEU A 113 ASN A 114 MET A 115 SITE 2 AC4 5 HOH A 301 SITE 1 AC5 4 HIS A 16 ALA A 20 ARG A 21 LYS B 163 SITE 1 AC6 3 LYS A 84 THR A 85 SER A 111 SITE 1 AC7 3 GLU A 9 HIS A 64 ASN A 114 SITE 1 AC8 5 ASP A 157 HIS A 158 PRO B 58 HIS B 59 SITE 2 AC8 5 ARG B 60 SITE 1 AC9 4 LYS A 163 HIS B 16 ALA B 20 ARG B 21 SITE 1 AD1 4 LEU B 82 LEU B 113 ASN B 114 MET B 115 SITE 1 AD2 3 GLU B 9 HIS B 64 ASN B 114 CRYST1 64.192 64.192 120.717 90.00 90.00 120.00 P 32 6 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 0.015578 0.008994 0.000000 0.00000 SCALE2 0.000000 0.017988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008284 0.00000