HEADER IMMUNE SYSTEM 31-MAY-16 5L6Q TITLE REFOLDED AL PROTEIN FROM CARDIAC AMYLOIDOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: H5AL; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 ORGAN: HEART; SOURCE 5 TISSUE: MUSCLE KEYWDS ANTIBODY, LIGHT CHAIN, SYSTEMIC AL AMYLOIDOSIS, AMYLOID FIBRILS, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.ANNAMALAI,F.LIBERTA,M.-T.VIELBERG,H.LILIE,K.-H.GUEHRS,A.SCHIERHORN, AUTHOR 2 R.KOEHLER,A.SCHMIDT,C.HAUPT,O.HEGENBART,S.SCHOENLAND,M.GROLL, AUTHOR 3 M.FAENDRICH REVDAT 4 10-JAN-24 5L6Q 1 LINK REVDAT 3 21-JUN-17 5L6Q 1 JRNL REVDAT 2 07-JUN-17 5L6Q 1 JRNL REVDAT 1 31-MAY-17 5L6Q 0 JRNL AUTH K.ANNAMALAI,F.LIBERTA,M.T.VIELBERG,W.CLOSE,H.LILIE, JRNL AUTH 2 K.H.GUHRS,A.SCHIERHORN,R.KOEHLER,A.SCHMIDT,C.HAUPT, JRNL AUTH 3 U.HEGENBART,S.SCHONLAND,M.SCHMIDT,M.GROLL,M.FANDRICH JRNL TITL COMMON FIBRIL STRUCTURES IMPLY SYSTEMICALLY CONSERVED JRNL TITL 2 PROTEIN MISFOLDING PATHWAYS IN VIVO. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 56 7510 2017 JRNL REFN ESSN 1521-3773 JRNL PMID 28544119 JRNL DOI 10.1002/ANIE.201701761 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 39847 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2098 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2883 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1604 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.89000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : 0.62000 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): 0.062 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.057 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.425 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1745 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1585 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2377 ; 1.668 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3663 ; 0.981 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 239 ; 6.472 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;35.586 ;23.816 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 270 ;11.079 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;13.530 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 260 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2083 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 415 ; 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): 903 ; 1.880 ; 1.366 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 902 ; 1.810 ; 1.361 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1138 ; 2.184 ; 2.057 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1139 ; 2.184 ; 2.059 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 842 ; 2.584 ; 1.795 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 842 ; 2.584 ; 1.795 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1232 ; 3.043 ; 2.521 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1994 ; 5.083 ;13.318 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1925 ; 3.594 ;12.556 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3330 ; 2.201 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 82 ;36.438 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3420 ;11.764 ; 5.000 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 : 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 1 A 108 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4319 6.1493 -11.9851 REMARK 3 T TENSOR REMARK 3 T11: 0.0236 T22: 0.0044 REMARK 3 T33: 0.0004 T12: -0.0001 REMARK 3 T13: -0.0003 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.0096 L22: 0.0216 REMARK 3 L33: 0.0236 L12: -0.0038 REMARK 3 L13: -0.0039 L23: 0.0153 REMARK 3 S TENSOR REMARK 3 S11: -0.0007 S12: -0.0005 S13: 0.0007 REMARK 3 S21: 0.0003 S22: -0.0002 S23: -0.0012 REMARK 3 S31: -0.0001 S32: -0.0017 S33: 0.0008 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 1 B 108 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3199 29.8133 -11.9313 REMARK 3 T TENSOR REMARK 3 T11: 0.0235 T22: 0.0047 REMARK 3 T33: 0.0002 T12: -0.0000 REMARK 3 T13: 0.0001 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.0093 L22: 0.0356 REMARK 3 L33: 0.0332 L12: -0.0012 REMARK 3 L13: 0.0014 L23: -0.0198 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: 0.0001 S13: 0.0002 REMARK 3 S21: 0.0007 S22: -0.0008 S23: 0.0019 REMARK 3 S31: 0.0000 S32: 0.0034 S33: 0.0001 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 5L6Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1200000218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT. SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42100 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: 4OD2 REMARK 200 REMARK 200 REMARK: ORTHORHOMBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 18% PEG 8000, 0.1 M ZINC REMARK 280 ACETATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 29.01000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.01000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.90500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -209.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 109 REMARK 465 PRO A 110 REMARK 465 LYS A 111 REMARK 465 ALA A 112 REMARK 465 ALA A 113 REMARK 465 PRO A 114 REMARK 465 SER A 115 REMARK 465 GLN B 109 REMARK 465 PRO B 110 REMARK 465 LYS B 111 REMARK 465 ALA B 112 REMARK 465 ALA B 113 REMARK 465 PRO B 114 REMARK 465 SER B 115 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 A 321 O HOH A 395 2.09 REMARK 500 OD2 ASP B 6 O HOH B 301 2.13 REMARK 500 NH1 ARG B 52 O HOH B 302 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 OE1 GLU A 79 O HOH A 395 1554 1.91 REMARK 500 OE1 GLU B 79 O HOH B 399 1554 2.09 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 ARG B 52 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 52 NE - CZ - NH2 ANGL. DEV. = -3.1 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 49 -53.78 80.38 REMARK 500 LYS B 49 -54.43 74.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 1 N REMARK 620 2 SER A 1 O 77.8 REMARK 620 3 ASP A 90 OD1 90.0 103.1 REMARK 620 4 HOH A 309 O 96.2 166.2 89.2 REMARK 620 5 HOH A 362 O 90.0 83.8 173.0 83.9 REMARK 620 6 HIS B 95 NE2 165.4 88.5 88.1 98.3 93.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 2 OE2 REMARK 620 2 GLU A 79 OE2 44.0 REMARK 620 3 CO3 A 206 O2 119.3 163.0 REMARK 620 4 HOH A 321 O 93.0 74.4 114.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 24 OD1 REMARK 620 2 ASP A 58 OD1 50.8 REMARK 620 3 HOH A 373 O 108.5 62.1 REMARK 620 4 HOH A 375 O 105.0 106.4 115.1 REMARK 620 5 HOH A 398 O 163.8 115.0 55.4 85.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 81 OE1 REMARK 620 2 HOH A 314 O 97.6 REMARK 620 3 HOH A 314 O 101.2 159.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 NE2 REMARK 620 2 SER B 1 N 167.0 REMARK 620 3 SER B 1 O 88.9 78.8 REMARK 620 4 ASP B 90 OD1 88.3 90.1 101.9 REMARK 620 5 HOH B 314 O 98.3 94.6 166.3 90.0 REMARK 620 6 HOH B 352 O 93.8 88.9 83.0 174.7 84.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 334 O REMARK 620 2 CO3 B 207 O1 101.6 REMARK 620 3 CO3 B 207 O2 147.8 46.3 REMARK 620 4 HOH B 328 O 91.1 101.7 94.6 REMARK 620 5 HOH B 377 O 104.7 84.2 76.9 161.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 320 O REMARK 620 2 CO3 B 207 O1 95.3 REMARK 620 3 CO3 B 207 O2 101.7 46.3 REMARK 620 4 HOH B 337 O 90.4 146.5 100.2 REMARK 620 5 HOH B 377 O 92.1 76.4 121.6 136.5 REMARK 620 6 HOH B 378 O 160.3 76.7 85.9 106.3 68.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 2 OE1 REMARK 620 2 GLU B 79 OE2 43.2 REMARK 620 3 CO3 B 208 O2 121.9 164.8 REMARK 620 4 HOH B 350 O 96.0 75.1 114.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 24 OD1 REMARK 620 2 ASP B 58 OD1 49.1 REMARK 620 3 HOH B 379 O 52.5 3.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 81 OE1 REMARK 620 2 GLU B 81 OE2 58.9 REMARK 620 N 1 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO3 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO3 B 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO3 B 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE B 209 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OD2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF AN ANTI-DR5 ANTIBODY BOUND REMARK 900 TO DR5 DBREF 5L6Q A 1 115 PDB 5L6Q 5L6Q 1 115 DBREF 5L6Q B 1 115 PDB 5L6Q 5L6Q 1 115 SEQRES 1 A 115 SER GLU LEU THR GLN ASP PRO ALA VAL SER VAL ALA LEU SEQRES 2 A 115 GLY GLN THR VAL ARG ILE THR CYS GLN GLY ASP SER LEU SEQRES 3 A 115 ARG SER TYR SER ALA SER TRP TYR GLN GLN LYS PRO GLY SEQRES 4 A 115 GLN ALA PRO VAL LEU VAL ILE PHE ARG LYS SER ASN ARG SEQRES 5 A 115 PRO SER GLY ILE PRO ASP ARG PHE SER GLY SER SER SER SEQRES 6 A 115 GLY ASN THR ALA SER LEU THR ILE THR GLY ALA GLN ALA SEQRES 7 A 115 GLU ASP GLU ALA ASP TYR TYR CYS ASN SER ARG ASP SER SEQRES 8 A 115 SER ALA ASN HIS GLN VAL PHE GLY GLY GLY THR LYS LEU SEQRES 9 A 115 THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SER SEQRES 1 B 115 SER GLU LEU THR GLN ASP PRO ALA VAL SER VAL ALA LEU SEQRES 2 B 115 GLY GLN THR VAL ARG ILE THR CYS GLN GLY ASP SER LEU SEQRES 3 B 115 ARG SER TYR SER ALA SER TRP TYR GLN GLN LYS PRO GLY SEQRES 4 B 115 GLN ALA PRO VAL LEU VAL ILE PHE ARG LYS SER ASN ARG SEQRES 5 B 115 PRO SER GLY ILE PRO ASP ARG PHE SER GLY SER SER SER SEQRES 6 B 115 GLY ASN THR ALA SER LEU THR ILE THR GLY ALA GLN ALA SEQRES 7 B 115 GLU ASP GLU ALA ASP TYR TYR CYS ASN SER ARG ASP SER SEQRES 8 B 115 SER ALA ASN HIS GLN VAL PHE GLY GLY GLY THR LYS LEU SEQRES 9 B 115 THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SER HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET ZN A 204 1 HET NA A 205 1 HET CO3 A 206 4 HET PEG A 207 7 HET ZN B 201 1 HET ZN B 202 1 HET ZN B 203 1 HET NA B 204 1 HET NA B 205 1 HET CL B 206 1 HET CO3 B 207 4 HET CO3 B 208 4 HET PGE B 209 10 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM CO3 CARBONATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CL CHLORIDE ION HETNAM PGE TRIETHYLENE GLYCOL FORMUL 3 ZN 7(ZN 2+) FORMUL 7 NA 3(NA 1+) FORMUL 8 CO3 3(C O3 2-) FORMUL 9 PEG C4 H10 O3 FORMUL 15 CL CL 1- FORMUL 18 PGE C6 H14 O4 FORMUL 19 HOH *199(H2 O) HELIX 1 AA1 ASP A 24 SER A 28 5 5 HELIX 2 AA2 GLN A 77 GLU A 81 5 5 HELIX 3 AA3 ASP B 24 SER B 28 5 5 HELIX 4 AA4 GLN B 77 GLU B 81 5 5 SHEET 1 AA1 4 THR A 4 GLN A 5 0 SHEET 2 AA1 4 THR A 16 GLN A 22 -1 O GLN A 22 N THR A 4 SHEET 3 AA1 4 THR A 68 THR A 74 -1 O LEU A 71 N ILE A 19 SHEET 4 AA1 4 PHE A 60 SER A 65 -1 N SER A 61 O THR A 72 SHEET 1 AA2 8 ALA A 8 ALA A 12 0 SHEET 2 AA2 8 THR A 102 LEU A 107 1 O LEU A 107 N VAL A 11 SHEET 3 AA2 8 ALA A 82 ARG A 89 -1 N ALA A 82 O LEU A 104 SHEET 4 AA2 8 HIS A 95 PHE A 98 -1 O VAL A 97 N SER A 88 SHEET 5 AA2 8 HIS B 95 PHE B 98 -1 O GLN B 96 N GLN A 96 SHEET 6 AA2 8 ALA B 82 ARG B 89 -1 N SER B 88 O VAL B 97 SHEET 7 AA2 8 THR B 102 LEU B 107 -1 O LEU B 104 N ALA B 82 SHEET 8 AA2 8 ALA B 8 ALA B 12 1 N VAL B 11 O LEU B 107 SHEET 1 AA3 8 VAL A 43 ILE A 46 0 SHEET 2 AA3 8 SER A 32 GLN A 36 -1 N GLN A 35 O VAL A 43 SHEET 3 AA3 8 ALA A 82 ARG A 89 -1 O ASP A 83 N GLN A 36 SHEET 4 AA3 8 HIS A 95 PHE A 98 -1 O VAL A 97 N SER A 88 SHEET 5 AA3 8 HIS B 95 PHE B 98 -1 O GLN B 96 N GLN A 96 SHEET 6 AA3 8 ALA B 82 ARG B 89 -1 N SER B 88 O VAL B 97 SHEET 7 AA3 8 SER B 32 GLN B 36 -1 N GLN B 36 O ASP B 83 SHEET 8 AA3 8 VAL B 43 ILE B 46 -1 O VAL B 43 N GLN B 35 SHEET 1 AA4 4 THR B 4 GLN B 5 0 SHEET 2 AA4 4 THR B 16 GLN B 22 -1 O GLN B 22 N THR B 4 SHEET 3 AA4 4 THR B 68 THR B 74 -1 O LEU B 71 N ILE B 19 SHEET 4 AA4 4 PHE B 60 SER B 65 -1 N SER B 61 O THR B 72 SSBOND 1 CYS A 21 CYS A 86 1555 1555 2.11 SSBOND 2 CYS B 21 CYS B 86 1555 1555 2.09 LINK N SER A 1 ZN ZN A 201 1555 1555 2.16 LINK O SER A 1 ZN ZN A 201 1555 1555 2.20 LINK OE2 GLU A 2 ZN ZN A 202 1555 1555 1.94 LINK OD1 ASP A 24 ZN ZN A 204 1555 1555 1.98 LINK OD1 ASP A 58 ZN ZN A 204 1555 1554 1.87 LINK OE2 GLU A 79 ZN ZN A 202 1555 1554 1.91 LINK OE1 GLU A 81 ZN ZN A 203 1555 1555 2.35 LINK OD1 ASP A 90 ZN ZN A 201 1555 1555 2.17 LINK NE2 HIS A 95 ZN ZN B 201 1555 1555 2.11 LINK ZN ZN A 201 O HOH A 309 1555 1555 2.07 LINK ZN ZN A 201 O HOH A 362 1555 1555 2.19 LINK ZN ZN A 201 NE2 HIS B 95 1555 1555 2.09 LINK ZN ZN A 202 O2 CO3 A 206 1555 1555 1.97 LINK ZN ZN A 202 O HOH A 321 1555 1555 1.78 LINK ZN ZN A 203 O HOH A 314 1555 1555 2.44 LINK ZN ZN A 203 O HOH A 314 1555 2655 1.87 LINK ZN ZN A 204 O HOH A 373 1555 1555 1.99 LINK ZN ZN A 204 O HOH A 375 1555 1555 2.28 LINK ZN ZN A 204 O HOH A 398 1555 1555 2.65 LINK NA NA A 205 O HOH A 334 1555 1555 1.97 LINK NA NA A 205 O1 CO3 B 207 1555 1555 2.07 LINK NA NA A 205 O2 CO3 B 207 1555 1555 2.99 LINK NA NA A 205 O HOH B 328 1555 1555 2.13 LINK NA NA A 205 O HOH B 377 1555 1555 2.59 LINK O HOH A 320 NA NA B 205 1555 1555 2.22 LINK N SER B 1 ZN ZN B 201 1555 1555 2.15 LINK O SER B 1 ZN ZN B 201 1555 1555 2.19 LINK OE1 GLU B 2 ZN ZN B 202 1555 1555 1.92 LINK OD1 ASP B 24 ZN ZN B 203 1555 1556 1.98 LINK OD1 ASP B 58 ZN ZN B 203 1555 1555 1.92 LINK OE2 GLU B 79 ZN ZN B 202 1555 1554 1.92 LINK OE1 GLU B 81 NA NA B 204 1555 1555 2.32 LINK OE2 GLU B 81 NA NA B 204 1555 1555 2.15 LINK OD1 ASP B 90 ZN ZN B 201 1555 1555 2.14 LINK ZN ZN B 201 O HOH B 314 1555 1555 2.12 LINK ZN ZN B 201 O HOH B 352 1555 1555 2.16 LINK ZN ZN B 202 O2 CO3 B 208 1555 1555 1.93 LINK ZN ZN B 202 O HOH B 350 1555 1555 1.92 LINK ZN ZN B 203 O HOH B 379 1555 1555 1.98 LINK NA NA B 205 O1 CO3 B 207 1555 1555 2.99 LINK NA NA B 205 O2 CO3 B 207 1555 1555 2.08 LINK NA NA B 205 O HOH B 337 1555 1555 1.92 LINK NA NA B 205 O HOH B 377 1555 1555 1.92 LINK NA NA B 205 O HOH B 378 1555 1555 2.55 SITE 1 AC1 5 SER A 1 ASP A 90 HOH A 309 HOH A 362 SITE 2 AC1 5 HIS B 95 SITE 1 AC2 5 GLU A 2 GLU A 79 CO3 A 206 HOH A 321 SITE 2 AC2 5 HOH A 395 SITE 1 AC3 3 GLU A 81 HOH A 314 HOH A 317 SITE 1 AC4 5 ASP A 24 ASP A 58 HOH A 373 HOH A 375 SITE 2 AC4 5 HOH A 398 SITE 1 AC5 6 HOH A 334 NA B 205 CO3 B 207 HOH B 328 SITE 2 AC5 6 HOH B 377 HOH B 378 SITE 1 AC6 5 GLU A 2 PRO A 57 GLU A 79 ZN A 202 SITE 2 AC6 5 HOH A 339 SITE 1 AC7 7 SER A 32 TYR A 34 ASN A 87 GLN A 96 SITE 2 AC7 7 HOH A 303 HOH A 336 PRO B 42 SITE 1 AC8 5 HIS A 95 SER B 1 ASP B 90 HOH B 314 SITE 2 AC8 5 HOH B 352 SITE 1 AC9 4 GLU B 2 GLU B 79 CO3 B 208 HOH B 350 SITE 1 AD1 4 ASP B 24 ASP B 58 CL B 206 HOH B 379 SITE 1 AD2 3 ARG B 48 GLU B 81 VAL B 106 SITE 1 AD3 6 NA A 205 HOH A 320 CO3 B 207 HOH B 337 SITE 2 AD3 6 HOH B 377 HOH B 378 SITE 1 AD4 5 ASP B 24 PRO B 57 ASP B 58 ARG B 59 SITE 2 AD4 5 ZN B 203 SITE 1 AD5 7 VAL A 43 LEU A 44 NA A 205 VAL B 43 SITE 2 AD5 7 LEU B 44 NA B 205 HOH B 337 SITE 1 AD6 5 GLU B 2 PRO B 57 GLU B 79 ZN B 202 SITE 2 AD6 5 HOH B 343 SITE 1 AD7 8 GLN A 36 PRO A 42 PHE A 98 SER B 32 SITE 2 AD7 8 TYR B 34 ASN B 87 GLN B 96 HOH B 368 CRYST1 58.020 105.810 34.750 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017235 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028777 0.00000