HEADER ENDOCYTOSIS 22-OCT-16 5M5V TITLE CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO A CLATHRIN-BOX MOTIF TITLE 2 FROM HEPATITIS D VIRUS LARGE ANTIGEN (CLADE 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLATHRIN HEAVY CHAIN 1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N-TERMINAL RESIDUES 'GS' ARE RESIDUAL FOLLOWING COMPND 6 CLEAVAGE OF THE PURIFICATION TAG; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LARGE DELTA ANTIGEN; COMPND 9 CHAIN: E, F, G, H, I, J; COMPND 10 FRAGMENT: CLATHRIN-BOX LIKE MOTIF, UNP RESIDUES 203-209; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: N- AND C-TERMINAL SERINE RESIDUES ARE NON-NATURAL AND COMPND 13 WERE ADDED TO ENHANCE SOLUBILITY SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: CLTC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPT3G; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HEPATITIS DELTA VIRUS; SOURCE 14 ORGANISM_COMMON: HDV; SOURCE 15 ORGANISM_TAXID: 12475 KEYWDS ENDOCYTOSIS, HEPATITIS DELTA VIRUS, HDAG-L EXPDTA X-RAY DIFFRACTION AUTHOR J.MUENZNER,S.C.GRAHAM REVDAT 3 17-JAN-24 5M5V 1 REMARK REVDAT 2 11-JAN-17 5M5V 1 JRNL REVDAT 1 23-NOV-16 5M5V 0 JRNL AUTH J.MUENZNER,L.M.TRAUB,B.T.KELLY,S.C.GRAHAM JRNL TITL CELLULAR AND VIRAL PEPTIDES BIND MULTIPLE SITES ON THE JRNL TITL 2 N-TERMINAL DOMAIN OF CLATHRIN. JRNL REF TRAFFIC V. 18 44 2017 JRNL REFN ESSN 1600-0854 JRNL PMID 27813245 JRNL DOI 10.1111/TRA.12457 REMARK 2 REMARK 2 RESOLUTION. 1.96 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 79976 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4224 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6057 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 279 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5862 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 583 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.51000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.697 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5999 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5850 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8135 ; 1.917 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13464 ; 1.096 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 748 ; 7.233 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 260 ;38.263 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1044 ;14.112 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;14.392 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 933 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6762 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1326 ; 0.005 ; 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): 3010 ; 1.767 ; 1.528 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3009 ; 1.767 ; 1.527 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3752 ; 2.805 ; 2.263 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3753 ; 2.805 ; 2.264 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2989 ; 2.494 ; 1.810 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2990 ; 2.494 ; 1.811 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4384 ; 3.907 ; 2.609 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6846 ; 8.246 ;13.572 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6847 ; 8.245 ;13.578 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 : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 4 363 B 4 363 23170 0.05 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 363 REMARK 3 ORIGIN FOR THE GROUP (A): 19.2550 0.4330 18.0130 REMARK 3 T TENSOR REMARK 3 T11: 0.0542 T22: 0.0872 REMARK 3 T33: 0.0436 T12: -0.0061 REMARK 3 T13: -0.0123 T23: -0.0369 REMARK 3 L TENSOR REMARK 3 L11: 1.5886 L22: 1.5490 REMARK 3 L33: 2.1459 L12: 0.2767 REMARK 3 L13: 0.7992 L23: 0.8775 REMARK 3 S TENSOR REMARK 3 S11: 0.0448 S12: -0.1586 S13: 0.1632 REMARK 3 S21: 0.0503 S22: 0.0358 S23: -0.1427 REMARK 3 S31: 0.0416 S32: 0.1861 S33: -0.0806 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 363 REMARK 3 ORIGIN FOR THE GROUP (A): 12.8430 19.9830 58.5110 REMARK 3 T TENSOR REMARK 3 T11: 0.1630 T22: 0.0551 REMARK 3 T33: 0.0277 T12: -0.0335 REMARK 3 T13: -0.0555 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 2.6295 L22: 1.4495 REMARK 3 L33: 1.3454 L12: 0.6358 REMARK 3 L13: 0.0365 L23: -0.3835 REMARK 3 S TENSOR REMARK 3 S11: 0.0447 S12: 0.1052 S13: 0.0940 REMARK 3 S21: -0.1768 S22: 0.0470 S23: 0.1415 REMARK 3 S31: 0.1903 S32: -0.1591 S33: -0.0916 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 REMARK 4 REMARK 4 5M5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-13 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : KB MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79976 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 39.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.58100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 1C9I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 NL PROTEIN:PEPTIDE (20 MG/ML NTD REMARK 280 AND 3.6 MM PEPTIDE) PLUS 400 NL RESERVOIR EQUILIBRATED AGAINST A REMARK 280 80 UL RESERVOIR OF 1.75 M SODIUM MALONATE PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 68.45000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 65.61500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.45000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 65.61500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, G, I 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F, H, J 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 748 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 762 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 536 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 -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 3 REMARK 465 SER E 1 REMARK 465 PRO E 2 REMARK 465 ARG E 3 REMARK 465 SER F 1 REMARK 465 PRO F 2 REMARK 465 ARG F 3 REMARK 465 SER G 1 REMARK 465 GLU G 8 REMARK 465 SER G 9 REMARK 465 SER H 1 REMARK 465 GLU H 8 REMARK 465 SER H 9 REMARK 465 SER I 1 REMARK 465 PRO I 2 REMARK 465 ARG I 3 REMARK 465 GLU I 8 REMARK 465 SER I 9 REMARK 465 SER J 1 REMARK 465 PRO J 2 REMARK 465 ARG J 3 REMARK 465 GLU J 8 REMARK 465 SER J 9 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 LEU E 4 CG CD1 CD2 REMARK 470 LEU F 4 CG CD1 CD2 REMARK 470 LEU I 4 CG CD1 CD2 REMARK 470 LEU J 4 CG CD1 CD2 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 O HOH B 472 O HOH B 604 1.81 REMARK 500 O HOH B 602 O HOH B 625 2.16 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 O HOH B 530 O HOH B 604 2657 1.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 107 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP B 107 CB - CG - OD1 ANGL. DEV. = 7.2 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 PRO A 237 154.68 -45.89 REMARK 500 PRO B 237 155.13 -45.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU F 4 PRO F 5 145.06 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 GOL A 401 DBREF 5M5V A 1 363 UNP P49951 CLH1_BOVIN 1 363 DBREF 5M5V B 1 363 UNP P49951 CLH1_BOVIN 1 363 DBREF 5M5V E 1 9 UNP A4ZNG7 A4ZNG7_HDV 202 210 DBREF 5M5V F 1 9 UNP A4ZNG7 A4ZNG7_HDV 202 210 DBREF 5M5V G 1 9 UNP A4ZNG7 A4ZNG7_HDV 202 210 DBREF 5M5V H 1 9 UNP A4ZNG7 A4ZNG7_HDV 202 210 DBREF 5M5V I 1 9 UNP A4ZNG7 A4ZNG7_HDV 202 210 DBREF 5M5V J 1 9 UNP A4ZNG7 A4ZNG7_HDV 202 210 SEQADV 5M5V GLY A -1 UNP P49951 EXPRESSION TAG SEQADV 5M5V SER A 0 UNP P49951 EXPRESSION TAG SEQADV 5M5V GLY B -1 UNP P49951 EXPRESSION TAG SEQADV 5M5V SER B 0 UNP P49951 EXPRESSION TAG SEQADV 5M5V SER E 1 UNP A4ZNG7 PRO 202 ENGINEERED MUTATION SEQADV 5M5V SER E 9 UNP A4ZNG7 CYS 210 ENGINEERED MUTATION SEQADV 5M5V SER F 1 UNP A4ZNG7 PRO 202 ENGINEERED MUTATION SEQADV 5M5V SER F 9 UNP A4ZNG7 CYS 210 ENGINEERED MUTATION SEQADV 5M5V SER G 1 UNP A4ZNG7 PRO 202 ENGINEERED MUTATION SEQADV 5M5V SER G 9 UNP A4ZNG7 CYS 210 ENGINEERED MUTATION SEQADV 5M5V SER H 1 UNP A4ZNG7 PRO 202 ENGINEERED MUTATION SEQADV 5M5V SER H 9 UNP A4ZNG7 CYS 210 ENGINEERED MUTATION SEQADV 5M5V SER I 1 UNP A4ZNG7 PRO 202 ENGINEERED MUTATION SEQADV 5M5V SER I 9 UNP A4ZNG7 CYS 210 ENGINEERED MUTATION SEQADV 5M5V SER J 1 UNP A4ZNG7 PRO 202 ENGINEERED MUTATION SEQADV 5M5V SER J 9 UNP A4ZNG7 CYS 210 ENGINEERED MUTATION SEQRES 1 A 365 GLY SER MET ALA GLN ILE LEU PRO ILE ARG PHE GLN GLU SEQRES 2 A 365 HIS LEU GLN LEU GLN ASN LEU GLY ILE ASN PRO ALA ASN SEQRES 3 A 365 ILE GLY PHE SER THR LEU THR MET GLU SER ASP LYS PHE SEQRES 4 A 365 ILE CYS ILE ARG GLU LYS VAL GLY GLU GLN ALA GLN VAL SEQRES 5 A 365 VAL ILE ILE ASP MET ASN ASP PRO SER ASN PRO ILE ARG SEQRES 6 A 365 ARG PRO ILE SER ALA ASP SER ALA ILE MET ASN PRO ALA SEQRES 7 A 365 SER LYS VAL ILE ALA LEU LYS ALA GLY LYS THR LEU GLN SEQRES 8 A 365 ILE PHE ASN ILE GLU MET LYS SER LYS MET LYS ALA HIS SEQRES 9 A 365 THR MET THR ASP ASP VAL THR PHE TRP LYS TRP ILE SER SEQRES 10 A 365 LEU ASN THR VAL ALA LEU VAL THR ASP ASN ALA VAL TYR SEQRES 11 A 365 HIS TRP SER MET GLU GLY GLU SER GLN PRO VAL LYS MET SEQRES 12 A 365 PHE ASP ARG HIS SER SER LEU ALA GLY CYS GLN ILE ILE SEQRES 13 A 365 ASN TYR ARG THR ASP ALA LYS GLN LYS TRP LEU LEU LEU SEQRES 14 A 365 THR GLY ILE SER ALA GLN GLN ASN ARG VAL VAL GLY ALA SEQRES 15 A 365 MET GLN LEU TYR SER VAL ASP ARG LYS VAL SER GLN PRO SEQRES 16 A 365 ILE GLU GLY HIS ALA ALA SER PHE ALA GLN PHE LYS MET SEQRES 17 A 365 GLU GLY ASN ALA GLU GLU SER THR LEU PHE CYS PHE ALA SEQRES 18 A 365 VAL ARG GLY GLN ALA GLY GLY LYS LEU HIS ILE ILE GLU SEQRES 19 A 365 VAL GLY THR PRO PRO THR GLY ASN GLN PRO PHE PRO LYS SEQRES 20 A 365 LYS ALA VAL ASP VAL PHE PHE PRO PRO GLU ALA GLN ASN SEQRES 21 A 365 ASP PHE PRO VAL ALA MET GLN ILE SER GLU LYS HIS ASP SEQRES 22 A 365 VAL VAL PHE LEU ILE THR LYS TYR GLY TYR ILE HIS LEU SEQRES 23 A 365 TYR ASP LEU GLU THR GLY THR CYS ILE TYR MET ASN ARG SEQRES 24 A 365 ILE SER GLY GLU THR ILE PHE VAL THR ALA PRO HIS GLU SEQRES 25 A 365 ALA THR ALA GLY ILE ILE GLY VAL ASN ARG LYS GLY GLN SEQRES 26 A 365 VAL LEU SER VAL CYS VAL GLU GLU GLU ASN ILE ILE PRO SEQRES 27 A 365 TYR ILE THR ASN VAL LEU GLN ASN PRO ASP LEU ALA LEU SEQRES 28 A 365 ARG MET ALA VAL ARG ASN ASN LEU ALA GLY ALA GLU GLU SEQRES 29 A 365 LEU SEQRES 1 B 365 GLY SER MET ALA GLN ILE LEU PRO ILE ARG PHE GLN GLU SEQRES 2 B 365 HIS LEU GLN LEU GLN ASN LEU GLY ILE ASN PRO ALA ASN SEQRES 3 B 365 ILE GLY PHE SER THR LEU THR MET GLU SER ASP LYS PHE SEQRES 4 B 365 ILE CYS ILE ARG GLU LYS VAL GLY GLU GLN ALA GLN VAL SEQRES 5 B 365 VAL ILE ILE ASP MET ASN ASP PRO SER ASN PRO ILE ARG SEQRES 6 B 365 ARG PRO ILE SER ALA ASP SER ALA ILE MET ASN PRO ALA SEQRES 7 B 365 SER LYS VAL ILE ALA LEU LYS ALA GLY LYS THR LEU GLN SEQRES 8 B 365 ILE PHE ASN ILE GLU MET LYS SER LYS MET LYS ALA HIS SEQRES 9 B 365 THR MET THR ASP ASP VAL THR PHE TRP LYS TRP ILE SER SEQRES 10 B 365 LEU ASN THR VAL ALA LEU VAL THR ASP ASN ALA VAL TYR SEQRES 11 B 365 HIS TRP SER MET GLU GLY GLU SER GLN PRO VAL LYS MET SEQRES 12 B 365 PHE ASP ARG HIS SER SER LEU ALA GLY CYS GLN ILE ILE SEQRES 13 B 365 ASN TYR ARG THR ASP ALA LYS GLN LYS TRP LEU LEU LEU SEQRES 14 B 365 THR GLY ILE SER ALA GLN GLN ASN ARG VAL VAL GLY ALA SEQRES 15 B 365 MET GLN LEU TYR SER VAL ASP ARG LYS VAL SER GLN PRO SEQRES 16 B 365 ILE GLU GLY HIS ALA ALA SER PHE ALA GLN PHE LYS MET SEQRES 17 B 365 GLU GLY ASN ALA GLU GLU SER THR LEU PHE CYS PHE ALA SEQRES 18 B 365 VAL ARG GLY GLN ALA GLY GLY LYS LEU HIS ILE ILE GLU SEQRES 19 B 365 VAL GLY THR PRO PRO THR GLY ASN GLN PRO PHE PRO LYS SEQRES 20 B 365 LYS ALA VAL ASP VAL PHE PHE PRO PRO GLU ALA GLN ASN SEQRES 21 B 365 ASP PHE PRO VAL ALA MET GLN ILE SER GLU LYS HIS ASP SEQRES 22 B 365 VAL VAL PHE LEU ILE THR LYS TYR GLY TYR ILE HIS LEU SEQRES 23 B 365 TYR ASP LEU GLU THR GLY THR CYS ILE TYR MET ASN ARG SEQRES 24 B 365 ILE SER GLY GLU THR ILE PHE VAL THR ALA PRO HIS GLU SEQRES 25 B 365 ALA THR ALA GLY ILE ILE GLY VAL ASN ARG LYS GLY GLN SEQRES 26 B 365 VAL LEU SER VAL CYS VAL GLU GLU GLU ASN ILE ILE PRO SEQRES 27 B 365 TYR ILE THR ASN VAL LEU GLN ASN PRO ASP LEU ALA LEU SEQRES 28 B 365 ARG MET ALA VAL ARG ASN ASN LEU ALA GLY ALA GLU GLU SEQRES 29 B 365 LEU SEQRES 1 E 9 SER PRO ARG LEU PRO LEU LEU GLU SER SEQRES 1 F 9 SER PRO ARG LEU PRO LEU LEU GLU SER SEQRES 1 G 9 SER PRO ARG LEU PRO LEU LEU GLU SER SEQRES 1 H 9 SER PRO ARG LEU PRO LEU LEU GLU SER SEQRES 1 I 9 SER PRO ARG LEU PRO LEU LEU GLU SER SEQRES 1 J 9 SER PRO ARG LEU PRO LEU LEU GLU SER HET GOL A 401 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 9 GOL C3 H8 O3 FORMUL 10 HOH *583(H2 O) HELIX 1 AA1 GLN A 16 GLY A 19 5 4 HELIX 2 AA2 ASN A 21 ILE A 25 5 5 HELIX 3 AA3 HIS A 145 ALA A 149 5 5 HELIX 4 AA4 PRO A 253 GLN A 257 5 5 HELIX 5 AA5 GLU A 310 ALA A 313 5 4 HELIX 6 AA6 ASN A 333 VAL A 341 1 9 HELIX 7 AA7 ASN A 344 ASN A 355 1 12 HELIX 8 AA8 GLN B 16 GLY B 19 5 4 HELIX 9 AA9 ASN B 21 ILE B 25 5 5 HELIX 10 AB1 HIS B 145 ALA B 149 5 5 HELIX 11 AB2 PRO B 253 GLN B 257 5 5 HELIX 12 AB3 GLU B 310 ALA B 313 5 4 HELIX 13 AB4 ASN B 333 VAL B 341 1 9 HELIX 14 AB5 ASN B 344 ASN B 356 1 13 SHEET 1 AA1 4 ILE A 7 GLN A 14 0 SHEET 2 AA1 4 GLN A 323 VAL A 329 -1 O VAL A 324 N LEU A 13 SHEET 3 AA1 4 GLY A 314 ASN A 319 -1 N GLY A 317 O LEU A 325 SHEET 4 AA1 4 ILE A 303 HIS A 309 -1 N ALA A 307 O ILE A 316 SHEET 1 AA2 4 LEU A 30 SER A 34 0 SHEET 2 AA2 4 PHE A 37 VAL A 44 -1 O CYS A 39 N THR A 31 SHEET 3 AA2 4 GLN A 47 ASP A 54 -1 O GLN A 49 N GLU A 42 SHEET 4 AA2 4 ILE A 62 PRO A 65 -1 O ILE A 62 N ILE A 52 SHEET 1 AA3 4 SER A 70 MET A 73 0 SHEET 2 AA3 4 VAL A 79 ALA A 84 -1 O ALA A 81 N ILE A 72 SHEET 3 AA3 4 THR A 87 ASN A 92 -1 O GLN A 89 N LEU A 82 SHEET 4 AA3 4 SER A 97 THR A 103 -1 O HIS A 102 N LEU A 88 SHEET 1 AA4 4 PHE A 110 TRP A 113 0 SHEET 2 AA4 4 THR A 118 VAL A 122 -1 O ALA A 120 N LYS A 112 SHEET 3 AA4 4 ALA A 126 SER A 131 -1 O TRP A 130 N VAL A 119 SHEET 4 AA4 4 VAL A 139 ASP A 143 -1 O MET A 141 N VAL A 127 SHEET 1 AA5 4 GLN A 152 THR A 158 0 SHEET 2 AA5 4 TRP A 164 GLN A 173 -1 O ILE A 170 N GLN A 152 SHEET 3 AA5 4 ARG A 176 SER A 185 -1 O ALA A 180 N GLY A 169 SHEET 4 AA5 4 VAL A 190 ILE A 194 -1 O ILE A 194 N MET A 181 SHEET 1 AA6 4 ALA A 198 PHE A 204 0 SHEET 2 AA6 4 SER A 213 ARG A 221 -1 O LEU A 215 N ALA A 202 SHEET 3 AA6 4 GLY A 226 GLU A 232 -1 O ILE A 231 N PHE A 216 SHEET 4 AA6 4 LYS A 246 VAL A 250 -1 O VAL A 248 N LEU A 228 SHEET 1 AA7 4 PRO A 261 SER A 267 0 SHEET 2 AA7 4 VAL A 272 THR A 277 -1 O PHE A 274 N GLN A 265 SHEET 3 AA7 4 TYR A 281 ASP A 286 -1 O TYR A 285 N VAL A 273 SHEET 4 AA7 4 CYS A 292 ARG A 297 -1 O ILE A 293 N LEU A 284 SHEET 1 AA8 4 ILE B 7 GLN B 14 0 SHEET 2 AA8 4 GLN B 323 VAL B 329 -1 O VAL B 324 N HIS B 12 SHEET 3 AA8 4 GLY B 314 ASN B 319 -1 N GLY B 317 O LEU B 325 SHEET 4 AA8 4 ILE B 303 HIS B 309 -1 N ALA B 307 O ILE B 316 SHEET 1 AA9 4 LEU B 30 SER B 34 0 SHEET 2 AA9 4 PHE B 37 VAL B 44 -1 O CYS B 39 N THR B 31 SHEET 3 AA9 4 GLN B 47 ASP B 54 -1 O ILE B 53 N ILE B 38 SHEET 4 AA9 4 ILE B 62 PRO B 65 -1 O ILE B 62 N ILE B 52 SHEET 1 AB1 4 SER B 70 MET B 73 0 SHEET 2 AB1 4 VAL B 79 ALA B 84 -1 O ALA B 81 N ILE B 72 SHEET 3 AB1 4 THR B 87 ASN B 92 -1 O GLN B 89 N LEU B 82 SHEET 4 AB1 4 SER B 97 THR B 103 -1 O LYS B 100 N ILE B 90 SHEET 1 AB2 4 VAL B 108 TRP B 113 0 SHEET 2 AB2 4 THR B 118 THR B 123 -1 O ALA B 120 N LYS B 112 SHEET 3 AB2 4 ALA B 126 SER B 131 -1 O TYR B 128 N LEU B 121 SHEET 4 AB2 4 VAL B 139 ASP B 143 -1 O VAL B 139 N HIS B 129 SHEET 1 AB3 4 GLN B 152 THR B 158 0 SHEET 2 AB3 4 TRP B 164 GLN B 173 -1 O ILE B 170 N GLN B 152 SHEET 3 AB3 4 ARG B 176 SER B 185 -1 O TYR B 184 N LEU B 165 SHEET 4 AB3 4 VAL B 190 ILE B 194 -1 O GLN B 192 N LEU B 183 SHEET 1 AB4 4 ALA B 198 PHE B 204 0 SHEET 2 AB4 4 SER B 213 ARG B 221 -1 O LEU B 215 N ALA B 202 SHEET 3 AB4 4 GLY B 226 GLU B 232 -1 O ILE B 231 N PHE B 216 SHEET 4 AB4 4 LYS B 246 VAL B 250 -1 O VAL B 248 N LEU B 228 SHEET 1 AB5 4 PRO B 261 SER B 267 0 SHEET 2 AB5 4 VAL B 272 THR B 277 -1 O PHE B 274 N GLN B 265 SHEET 3 AB5 4 TYR B 281 ASP B 286 -1 O TYR B 285 N VAL B 273 SHEET 4 AB5 4 CYS B 292 ARG B 297 -1 O ILE B 293 N LEU B 284 SITE 1 AC1 7 HIS A 102 MET A 104 THR A 105 ASP A 106 SITE 2 AC1 7 TYR A 128 HOH A 589 HOH A 619 CRYST1 136.900 131.230 78.450 90.00 115.86 90.00 C 1 2 1 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 0.007305 0.000000 0.003541 0.00000 SCALE2 0.000000 0.007620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014165 0.00000